X-PLOR: V3.840 user: on: Alpha/OSF at: 16-Aug-96 18:13:27 Author: Axel T. Brunger Copyright: 1988-96 (Yale University), 1987 (Harvard University) X-PLOR>! dgsa.inp -- Clean up the output of dg.inp using simulated annealing X-PLOR>! Dave Schweisguth , 22 Jul 1996 X-PLOR>! Derived from nmr/dgsa.inp X-PLOR> X-PLOR>evaluate ($init_t=3000) ! Temperature for constant-temperature MD EVALUATE: symbol $INIT_T set to 3000.00 (real) X-PLOR>evaluate ($high_steps=6000) ! Number of steps at high temp EVALUATE: symbol $HIGH_STEPS set to 6000.00 (real) X-PLOR>evaluate ($high_timestep=0.002) ! Time of each MD step at high temp EVALUATE: symbol $HIGH_TIMESTEP set to 0.200000E-02 (real) X-PLOR>evaluate ($final_t=300) ! Final temperature EVALUATE: symbol $FINAL_T set to 300.000 (real) X-PLOR>evaluate ($cool_steps=7500) ! Number of steps for cooling EVALUATE: symbol $COOL_STEPS set to 7500.00 (real) X-PLOR>evaluate ($cool_timestep=0.002) ! Time of each MD step when cooling EVALUATE: symbol $COOL_TIMESTEP set to 0.200000E-02 (real) X-PLOR>evaluate ($tempstep=50) ! Degree increment for cooling EVALUATE: symbol $TEMPSTEP set to 50.0000 (real) X-PLOR> X-PLOR>set seed=@xplor.seed end ! Use 'xplor -s' ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/xplor.seed opened. SEED=46164.0791931152 SET> end ! Use 'xplor -s' X-PLOR> X-PLOR>set echo=off message=off end ! Normal use REMARKS FILENAME="/sgi/people/dcs/ws/xplor/italy2.4x/rsf.inp" REMARKS DATE:27-Apr-96 13:37:21 created by user: XPLOR: current counts (number in parenthesis is maximum) NATOM= 677(MAXA= 96000) NBOND= 728(MAXB= 96000) NTHETA= 1299(MAXT= 144000) NGRP= 218(MAXGRP= 96000) NPHI= 0(MAXP= 180000) NIMPHI= 461(MAXIMP= 96000) NDON= 68(MAXPAD= 24000) NACC= 105(MAXPAD= 24000) NNB= 63(MAXNB= 18000) NOE: allocating space for 1000 restraints. XREFIN: allocating space for 300 assignments. X-PLOR> X-PLOR>vector do (fbeta=10) (all) ! Friction coeff. for MD heatbath, in 1/ps. SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (mass=100) (all) ! Uniform heavy masses to speed MD. SELRPN: 677 atoms have been selected out of 677 X-PLOR> X-PLOR>noe ! Parameters for NOE effective energy term. NOE> ceiling=1000 NOE> averaging * cent NOE> potential * square NOE> sqconstant * 1 NOE> sqexponent * 2 NOE> scale * 100 ! Constant NOE scale throughout the protocol. NOE>end X-PLOR> X-PLOR>parameter ! Parameters for the repulsive energy term. PARRDR> nbonds NBDSET> repel=0.5 ! Initial value for repel--modified later. NBDSET> rexp=2 NBDSET> irexp=2 NBDSET> rcon=1 NBDSET> nbxmod=-2 ! Initial value for nbxmod--modified later. NBDSET> wmin=0.01 NBDSET> cutnb=4.5 NBDSET> ctonnb=2.99 NBDSET> ctofnb=3 NBDSET> tolerance=0.5 NBDSET> end PARRDR>end X-PLOR> X-PLOR>! Test for the correct enantiomer; if you want to bypass this test because X-PLOR>! the substructures were tested previously, simply remove the -1 from the X-PLOR>! next statement. X-PLOR> X-PLOR>for $image in (1 -1) loop imag FOR LOOP: symbol IMAGE set to 1.00000 (real) X-PLOR> X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @dg.pdb ! END in PDB file ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/dg.pdb opened. COOR>REMARK FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/dg.pdb" COOR>REMARK DATE:16-Aug-96 18:13:27 created by user: COOR>ATOM 1 P GUA 1 10.530 3.172 10.479 1.00 0.00 A COOR>ATOM 2 O1P GUA 1 13.528 5.873 7.438 1.00 0.00 A X-PLOR> ! END in PDB file X-PLOR> vector do (x=x * $image) (known) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector identity (store1) (not known) ! Set store1 to unknowns. SELRPN: 0 atoms have been selected out of 677 X-PLOR> X-PLOR> ! Create local ideal geometry by template fitting; X-PLOR> ! this also takes care of unknown atoms. X-PLOR> X-PLOR> coordinates copy end ! Store current coordinates in comparison set. COOR: selected main coordinates copied to comp X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @template.pdb ! END in PDB file ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/template.pdb opened. COOR>REMARK 5 FILENAME="/sgi/people/dcs/ws/xplor/italy2.4x/template.pdb" COOR>REMARK 5 DATE:27-Apr-96 13:42:54 created by user: COOR>ATOM 1 P GUA A 1 -7.862 1.642 2.093 1.00 0.00 A COOR>ATOM 2 O1P GUA A 1 -9.267 1.385 1.685 1.00 0.00 A X-PLOR> ! END in PDB file X-PLOR> X-PLOR> set echo=off message=off end R.m.s. diff. between fitted set and comp. set for selected atoms = 2.4100 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.8012 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1248 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2865 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.3392 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.4941 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.7071 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.3220 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.9781 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.9275 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.6854 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.6603 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.0903 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.3887 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0775 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.4398 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8732 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8381 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.7694 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0581 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6370 X-PLOR> X-PLOR> coordinates swap end COOR: selected coordinates swaped (main<->comp) X-PLOR> X-PLOR> ! Minimization of bonds, VDWs, and NOEs. X-PLOR> X-PLOR> flags exclude * include bond vdw noe cdih plan end X-PLOR> constraints interaction (all) (all) weights * 1 vdw 20 end end SELRPN: 677 atoms have been selected out of 677 SELRPN: 677 atoms have been selected out of 677 X-PLOR> parameter nbonds nbxmod=-2 repel=0.5 end end X-PLOR> restraints dihedral scale=20 end X-PLOR> minimize powell drop=10 nstep=300 nprint=10 end POWELL: number of degrees of freedom= 2031 CODBON: bond type-based parameters retrieved NBUPDA: type-based van der Waals parameters retrieved. NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 728 exclusions and 0 interactions(1-4) NBONDS: found 14959 intra-atom interactions NBONDS: found 15024 intra-atom interactions NBONDS: found 15182 intra-atom interactions NBONDS: found 15265 intra-atom interactions NBONDS: found 15464 intra-atom interactions NBONDS: found 15675 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0002 ----------------------- | Etotal =110406.937 grad(E)=303.309 E(BOND)=10934.086 E(VDW )=10071.265 | | E(CDIH)=4657.830 E(NOE )=84188.159 E(PLAN)=555.597 | ------------------------------------------------------------------------------- NBONDS: found 15765 intra-atom interactions NBONDS: found 15831 intra-atom interactions NBONDS: found 15900 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0002 ----------------------- | Etotal =64778.525 grad(E)=192.171 E(BOND)=4827.958 E(VDW )=8565.691 | | E(CDIH)=3520.776 E(NOE )=47461.226 E(PLAN)=402.874 | ------------------------------------------------------------------------------- NBONDS: found 15943 intra-atom interactions NBONDS: found 15975 intra-atom interactions NBONDS: found 15971 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0002 ----------------------- | Etotal =47428.732 grad(E)=163.017 E(BOND)=2878.651 E(VDW )=6690.172 | | E(CDIH)=3001.555 E(NOE )=34575.441 E(PLAN)=282.912 | ------------------------------------------------------------------------------- NBONDS: found 15928 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =37277.688 grad(E)=92.639 E(BOND)=1512.061 E(VDW )=4521.550 | | E(CDIH)=2590.226 E(NOE )=28389.249 E(PLAN)=264.602 | ------------------------------------------------------------------------------- NBONDS: found 15799 intra-atom interactions NBONDS: found 15823 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =31612.107 grad(E)=89.183 E(BOND)=1273.923 E(VDW )=3416.418 | | E(CDIH)=2315.808 E(NOE )=24323.166 E(PLAN)=282.791 | ------------------------------------------------------------------------------- NBONDS: found 15734 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0000 ----------------------- | Etotal =27029.657 grad(E)=71.389 E(BOND)=1038.437 E(VDW )=2508.038 | | E(CDIH)=2088.500 E(NOE )=21097.796 E(PLAN)=296.886 | ------------------------------------------------------------------------------- NBONDS: found 15634 intra-atom interactions NBONDS: found 15529 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0000 ----------------------- | Etotal =23462.184 grad(E)=54.313 E(BOND)=587.522 E(VDW )=1978.570 | | E(CDIH)=1941.886 E(NOE )=18698.721 E(PLAN)=255.485 | ------------------------------------------------------------------------------- NBONDS: found 15425 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0000 ----------------------- | Etotal =22114.551 grad(E)=49.410 E(BOND)=605.963 E(VDW )=1809.119 | | E(CDIH)=1778.870 E(NOE )=17676.336 E(PLAN)=244.263 | ------------------------------------------------------------------------------- NBONDS: found 15392 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0000 ----------------------- | Etotal =20707.771 grad(E)=44.357 E(BOND)=471.577 E(VDW )=1606.014 | | E(CDIH)=1805.646 E(NOE )=16579.378 E(PLAN)=245.156 | ------------------------------------------------------------------------------- NBONDS: found 15213 intra-atom interactions NBONDS: found 15391 intra-atom interactions NBONDS: found 15284 intra-atom interactions NBONDS: found 15362 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =20064.862 grad(E)=57.895 E(BOND)=464.495 E(VDW )=1443.993 | | E(CDIH)=1930.523 E(NOE )=15980.843 E(PLAN)=245.009 | ------------------------------------------------------------------------------- --------------- cycle= 110 ------ stepsize= 0.0000 ----------------------- | Etotal =19017.429 grad(E)=31.065 E(BOND)=375.739 E(VDW )=1273.777 | | E(CDIH)=1655.055 E(NOE )=15478.457 E(PLAN)=234.401 | ------------------------------------------------------------------------------- --------------- cycle= 120 ------ stepsize= 0.0000 ----------------------- | Etotal =19009.160 grad(E)=31.308 E(BOND)=380.132 E(VDW )=1271.627 | | E(CDIH)=1652.384 E(NOE )=15470.840 E(PLAN)=234.177 | ------------------------------------------------------------------------------- --------------- cycle= 130 ------ stepsize= 0.0000 ----------------------- | Etotal =19008.984 grad(E)=31.316 E(BOND)=380.245 E(VDW )=1271.579 | | E(CDIH)=1652.324 E(NOE )=15470.665 E(PLAN)=234.172 | ------------------------------------------------------------------------------- --------------- cycle= 140 ------ stepsize= 0.0000 ----------------------- | Etotal =19214.906 grad(E)=53.881 E(BOND)=380.248 E(VDW )=1271.577 | | E(CDIH)=1858.249 E(NOE )=15470.661 E(PLAN)=234.172 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =19214.907 grad(E)=53.881 E(BOND)=380.248 E(VDW )=1271.577 | | E(CDIH)=1858.249 E(NOE )=15470.661 E(PLAN)=234.172 | ------------------------------------------------------------------------------- %POWELL-ERR: Line search abandoned POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR> ! Include angles. X-PLOR> X-PLOR> flags include angl end X-PLOR> minimize powell drop=10 nstep=300 nprint=10 end POWELL: number of degrees of freedom= 2031 CODANG: angle type-based parameters retrieved NBONDS: found 15323 intra-atom interactions NBONDS: found 15235 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =110377.191 grad(E)=337.252 E(BOND)=12319.380 E(ANGL)=70924.033 | | E(VDW )=2991.277 E(CDIH)=3322.447 E(NOE )=20424.429 E(PLAN)=395.626 | ------------------------------------------------------------------------------- NBONDS: found 15240 intra-atom interactions NBONDS: found 15268 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =75833.476 grad(E)=175.581 E(BOND)=4401.903 E(ANGL)=39563.086 | | E(VDW )=3301.321 E(CDIH)=3791.716 E(NOE )=24322.686 E(PLAN)=452.764 | ------------------------------------------------------------------------------- NBONDS: found 15232 intra-atom interactions NBONDS: found 15209 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =63956.274 grad(E)=141.522 E(BOND)=2553.269 E(ANGL)=28362.091 | | E(VDW )=3361.415 E(CDIH)=4032.477 E(NOE )=25137.870 E(PLAN)=509.152 | ------------------------------------------------------------------------------- NBONDS: found 15110 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =58329.896 grad(E)=93.159 E(BOND)=2329.623 E(ANGL)=24154.828 | | E(VDW )=3295.593 E(CDIH)=3984.635 E(NOE )=24035.694 E(PLAN)=529.524 | ------------------------------------------------------------------------------- NBONDS: found 15043 intra-atom interactions NBONDS: found 14981 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =53388.389 grad(E)=90.846 E(BOND)=1964.856 E(ANGL)=19839.813 | | E(VDW )=3062.454 E(CDIH)=4024.815 E(NOE )=23941.845 E(PLAN)=554.607 | ------------------------------------------------------------------------------- NBONDS: found 14934 intra-atom interactions NBONDS: found 14861 intra-atom interactions NBONDS: found 14778 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =48419.341 grad(E)=76.992 E(BOND)=1936.279 E(ANGL)=16470.169 | | E(VDW )=2557.652 E(CDIH)=4097.891 E(NOE )=22804.314 E(PLAN)=553.035 | ------------------------------------------------------------------------------- NBONDS: found 14714 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =44941.820 grad(E)=61.893 E(BOND)=1700.816 E(ANGL)=14696.996 | | E(VDW )=2305.532 E(CDIH)=3997.723 E(NOE )=21703.438 E(PLAN)=537.315 | ------------------------------------------------------------------------------- NBONDS: found 14679 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =43221.591 grad(E)=52.573 E(BOND)=1699.297 E(ANGL)=14056.598 | | E(VDW )=2181.554 E(CDIH)=3827.390 E(NOE )=20937.871 E(PLAN)=518.881 | ------------------------------------------------------------------------------- NBONDS: found 14566 intra-atom interactions NBONDS: found 14505 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =41627.017 grad(E)=48.282 E(BOND)=1571.426 E(ANGL)=13327.882 | | E(VDW )=2062.986 E(CDIH)=3730.591 E(NOE )=20420.040 E(PLAN)=514.091 | ------------------------------------------------------------------------------- NBONDS: found 14438 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =40127.630 grad(E)=39.114 E(BOND)=1376.997 E(ANGL)=12415.357 | | E(VDW )=1997.542 E(CDIH)=3653.617 E(NOE )=20154.591 E(PLAN)=529.525 | ------------------------------------------------------------------------------- NBONDS: found 14375 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0001 ----------------------- | Etotal =39057.118 grad(E)=41.118 E(BOND)=1291.242 E(ANGL)=11852.968 | | E(VDW )=1921.480 E(CDIH)=3728.311 E(NOE )=19727.740 E(PLAN)=535.378 | ------------------------------------------------------------------------------- NBONDS: found 14284 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0001 ----------------------- | Etotal =38163.645 grad(E)=42.458 E(BOND)=1292.413 E(ANGL)=11630.074 | | E(VDW )=1877.381 E(CDIH)=3672.612 E(NOE )=19163.311 E(PLAN)=527.853 | ------------------------------------------------------------------------------- NBONDS: found 14153 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0001 ----------------------- | Etotal =37298.981 grad(E)=37.434 E(BOND)=1304.745 E(ANGL)=11420.481 | | E(VDW )=1873.924 E(CDIH)=3601.804 E(NOE )=18578.484 E(PLAN)=519.545 | ------------------------------------------------------------------------------- NBONDS: found 14019 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0001 ----------------------- | Etotal =36467.599 grad(E)=35.929 E(BOND)=1282.157 E(ANGL)=11139.718 | | E(VDW )=1807.439 E(CDIH)=3612.112 E(NOE )=18101.030 E(PLAN)=525.144 | ------------------------------------------------------------------------------- NBONDS: found 13901 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =35808.709 grad(E)=35.232 E(BOND)=1251.738 E(ANGL)=10984.302 | | E(VDW )=1671.558 E(CDIH)=3541.998 E(NOE )=17846.257 E(PLAN)=512.856 | ------------------------------------------------------------------------------- NBONDS: found 13772 intra-atom interactions --------------- cycle= 160 ------ stepsize= 0.0001 ----------------------- | Etotal =35303.577 grad(E)=28.570 E(BOND)=1162.294 E(ANGL)=10878.130 | | E(VDW )=1622.904 E(CDIH)=3471.842 E(NOE )=17668.001 E(PLAN)=500.408 | ------------------------------------------------------------------------------- NBONDS: found 13670 intra-atom interactions --------------- cycle= 170 ------ stepsize= 0.0001 ----------------------- | Etotal =34884.014 grad(E)=22.134 E(BOND)=1157.595 E(ANGL)=10775.844 | | E(VDW )=1609.663 E(CDIH)=3453.496 E(NOE )=17407.868 E(PLAN)=479.549 | ------------------------------------------------------------------------------- NBONDS: found 13507 intra-atom interactions --------------- cycle= 180 ------ stepsize= 0.0001 ----------------------- | Etotal =34177.412 grad(E)=33.387 E(BOND)=1168.680 E(ANGL)=10552.027 | | E(VDW )=1489.596 E(CDIH)=3452.208 E(NOE )=17050.436 E(PLAN)=464.466 | ------------------------------------------------------------------------------- NBONDS: found 13439 intra-atom interactions --------------- cycle= 190 ------ stepsize= 0.0001 ----------------------- | Etotal =33401.599 grad(E)=37.118 E(BOND)=1186.629 E(ANGL)=10161.735 | | E(VDW )=1373.275 E(CDIH)=3467.924 E(NOE )=16761.824 E(PLAN)=450.212 | ------------------------------------------------------------------------------- NBONDS: found 13329 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =32706.494 grad(E)=33.152 E(BOND)=1106.231 E(ANGL)=9972.708 | | E(VDW )=1298.825 E(CDIH)=3471.248 E(NOE )=16421.191 E(PLAN)=436.292 | ------------------------------------------------------------------------------- NBONDS: found 13182 intra-atom interactions --------------- cycle= 210 ------ stepsize= 0.0001 ----------------------- | Etotal =32201.576 grad(E)=26.931 E(BOND)=1085.702 E(ANGL)=9835.279 | | E(VDW )=1269.898 E(CDIH)=3481.901 E(NOE )=16097.390 E(PLAN)=431.406 | ------------------------------------------------------------------------------- --------------- cycle= 220 ------ stepsize= 0.0001 ----------------------- | Etotal =31849.897 grad(E)=27.928 E(BOND)=1053.577 E(ANGL)=9647.805 | | E(VDW )=1263.412 E(CDIH)=3477.590 E(NOE )=15978.415 E(PLAN)=429.098 | ------------------------------------------------------------------------------- NBONDS: found 13078 intra-atom interactions --------------- cycle= 230 ------ stepsize= 0.0001 ----------------------- | Etotal =31464.809 grad(E)=22.688 E(BOND)=1017.019 E(ANGL)=9423.808 | | E(VDW )=1254.000 E(CDIH)=3467.743 E(NOE )=15871.516 E(PLAN)=430.723 | ------------------------------------------------------------------------------- NBONDS: found 13053 intra-atom interactions --------------- cycle= 240 ------ stepsize= 0.0001 ----------------------- | Etotal =31185.916 grad(E)=20.090 E(BOND)=995.205 E(ANGL)=9261.640 | | E(VDW )=1242.006 E(CDIH)=3460.753 E(NOE )=15795.633 E(PLAN)=430.678 | ------------------------------------------------------------------------------- NBONDS: found 13021 intra-atom interactions --------------- cycle= 250 ------ stepsize= 0.0001 ----------------------- | Etotal =30978.855 grad(E)=17.960 E(BOND)=947.160 E(ANGL)=9185.817 | | E(VDW )=1252.786 E(CDIH)=3455.782 E(NOE )=15712.736 E(PLAN)=424.575 | ------------------------------------------------------------------------------- --------------- cycle= 260 ------ stepsize= 0.0001 ----------------------- | Etotal =30813.002 grad(E)=13.513 E(BOND)=951.862 E(ANGL)=9120.922 | | E(VDW )=1242.508 E(CDIH)=3460.933 E(NOE )=15620.857 E(PLAN)=415.920 | ------------------------------------------------------------------------------- NBONDS: found 12952 intra-atom interactions --------------- cycle= 270 ------ stepsize= 0.0001 ----------------------- | Etotal =30600.007 grad(E)=22.661 E(BOND)=954.037 E(ANGL)=9146.601 | | E(VDW )=1192.887 E(CDIH)=3451.450 E(NOE )=15445.462 E(PLAN)=409.571 | ------------------------------------------------------------------------------- --------------- cycle= 280 ------ stepsize= 0.0001 ----------------------- | Etotal =30369.508 grad(E)=20.306 E(BOND)=935.611 E(ANGL)=9155.161 | | E(VDW )=1182.956 E(CDIH)=3435.209 E(NOE )=15256.875 E(PLAN)=403.697 | ------------------------------------------------------------------------------- NBONDS: found 12887 intra-atom interactions --------------- cycle= 290 ------ stepsize= 0.0001 ----------------------- | Etotal =30216.445 grad(E)=16.057 E(BOND)=909.376 E(ANGL)=9163.864 | | E(VDW )=1201.097 E(CDIH)=3417.014 E(NOE )=15130.976 E(PLAN)=394.118 | ------------------------------------------------------------------------------- NBONDS: found 12828 intra-atom interactions --------------- cycle= 300 ------ stepsize= 0.0001 ----------------------- | Etotal =30045.612 grad(E)=17.313 E(BOND)=888.804 E(ANGL)=9120.095 | | E(VDW )=1227.406 E(CDIH)=3398.911 E(NOE )=15024.475 E(PLAN)=385.922 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR> ! Dynamics, slowly introducing dihedral and improper angles X-PLOR> X-PLOR> flags include dihe impr end X-PLOR> X-PLOR> evaluate ($nstep1=int($high_steps/8)) ! Dynamics runs 1, 2, 3 and 5 EVALUATE: symbol $NSTEP1 set to 750.000 (real) X-PLOR> evaluate ($nstep2=int($high_steps/2)) ! Dynamics run 4 EVALUATE: symbol $NSTEP2 set to 3000.00 (real) X-PLOR> X-PLOR> constraints inter (all) (all) weights * 0.1 dihe 0.05 impr 0.05 vdw 20 end end SELRPN: 677 atoms have been selected out of 677 SELRPN: 677 atoms have been selected out of 677 X-PLOR> dynamics verlet DYNAmics> nstep=$nstep1 time=$high_timestep iasvel=maxwell firstt=$init_t DYNAmics> tcoup=true tbath=$init_t nprint=100 iprfrq=0 DYNAmics> end DYNAMC: number of degrees of freedom= 2031 ASSVEL: velocities assigned at 3000.0000 K, SEED= 14887201.5 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : -0.00001 0.00001 -0.00001 velocity [A/ps] : -0.14118 -0.12570 0.00810 ang. mom. [amu A/ps] : -26605.46353 6562.16818 286275.73316 kin. ener. [Kcal/mol] : 2.89615 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : -0.00001 0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 CODIMP: improper type-based parameters retrieved NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 728 exclusions and 0 interactions(1-4) NBONDS: found 12823 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=39499.765 E(kin)=5864.171 temperature=2905.943 | | Etotal =33635.595 grad(E)=105.688 E(BOND)=88.880 E(ANGL)=912.009 | | E(DIHE)=0.000 E(IMPR)=12597.991 E(VDW )=1227.406 E(CDIH)=3398.911 | | E(NOE )=15024.475 E(PLAN)=385.922 | ------------------------------------------------------------------------------- NBONDS: found 12836 intra-atom interactions NBONDS: found 12841 intra-atom interactions NBONDS: found 12756 intra-atom interactions NBONDS: found 12751 intra-atom interactions NBONDS: found 12739 intra-atom interactions NBONDS: found 12729 intra-atom interactions NBONDS: found 12709 intra-atom interactions NBONDS: found 12672 intra-atom interactions NBONDS: found 12634 intra-atom interactions NBONDS: found 12589 intra-atom interactions NBONDS: found 12544 intra-atom interactions NBONDS: found 12524 intra-atom interactions NBONDS: found 12470 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=33666.360 E(kin)=7449.624 temperature=3691.601 | | Etotal =26216.736 grad(E)=72.704 E(BOND)=3019.720 E(ANGL)=5208.099 | | E(DIHE)=0.000 E(IMPR)=6189.508 E(VDW )=642.623 E(CDIH)=1953.782 | | E(NOE )=8889.513 E(PLAN)=313.491 | ------------------------------------------------------------------------------- NBONDS: found 12404 intra-atom interactions NBONDS: found 12338 intra-atom interactions NBONDS: found 12341 intra-atom interactions NBONDS: found 12257 intra-atom interactions NBONDS: found 12200 intra-atom interactions NBONDS: found 12151 intra-atom interactions NBONDS: found 12122 intra-atom interactions NBONDS: found 12042 intra-atom interactions NBONDS: found 11979 intra-atom interactions NBONDS: found 11947 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=30793.371 E(kin)=6354.713 temperature=3149.027 | | Etotal =24438.657 grad(E)=69.389 E(BOND)=2774.538 E(ANGL)=5135.699 | | E(DIHE)=0.000 E(IMPR)=5554.017 E(VDW )=590.550 E(CDIH)=1867.752 | | E(NOE )=8223.096 E(PLAN)=293.007 | ------------------------------------------------------------------------------- NBONDS: found 11918 intra-atom interactions NBONDS: found 11886 intra-atom interactions NBONDS: found 11833 intra-atom interactions NBONDS: found 11767 intra-atom interactions NBONDS: found 11742 intra-atom interactions NBONDS: found 11720 intra-atom interactions NBONDS: found 11708 intra-atom interactions NBONDS: found 11706 intra-atom interactions NBONDS: found 11717 intra-atom interactions NBONDS: found 11665 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=29359.534 E(kin)=6019.575 temperature=2982.952 | | Etotal =23339.959 grad(E)=68.336 E(BOND)=3410.941 E(ANGL)=4799.344 | | E(DIHE)=0.000 E(IMPR)=5102.970 E(VDW )=564.972 E(CDIH)=1658.075 | | E(NOE )=7484.316 E(PLAN)=319.342 | ------------------------------------------------------------------------------- NBONDS: found 11736 intra-atom interactions NBONDS: found 11777 intra-atom interactions NBONDS: found 11777 intra-atom interactions NBONDS: found 11752 intra-atom interactions NBONDS: found 11737 intra-atom interactions NBONDS: found 11717 intra-atom interactions NBONDS: found 11721 intra-atom interactions NBONDS: found 11702 intra-atom interactions NBONDS: found 11724 intra-atom interactions NBONDS: found 11704 intra-atom interactions NBONDS: found 11710 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=28708.617 E(kin)=6292.694 temperature=3118.294 | | Etotal =22415.923 grad(E)=67.931 E(BOND)=3318.441 E(ANGL)=4621.650 | | E(DIHE)=0.000 E(IMPR)=4620.826 E(VDW )=521.330 E(CDIH)=1585.251 | | E(NOE )=7460.202 E(PLAN)=288.223 | ------------------------------------------------------------------------------- NBONDS: found 11665 intra-atom interactions NBONDS: found 11671 intra-atom interactions NBONDS: found 11641 intra-atom interactions NBONDS: found 11605 intra-atom interactions NBONDS: found 11610 intra-atom interactions NBONDS: found 11573 intra-atom interactions NBONDS: found 11536 intra-atom interactions NBONDS: found 11492 intra-atom interactions NBONDS: found 11475 intra-atom interactions NBONDS: found 11482 intra-atom interactions NBONDS: found 11474 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=28114.956 E(kin)=6337.141 temperature=3140.320 | | Etotal =21777.815 grad(E)=66.579 E(BOND)=2838.509 E(ANGL)=4671.108 | | E(DIHE)=0.000 E(IMPR)=4911.678 E(VDW )=461.443 E(CDIH)=1319.402 | | E(NOE )=7484.113 E(PLAN)=91.562 | ------------------------------------------------------------------------------- NBONDS: found 11476 intra-atom interactions NBONDS: found 11492 intra-atom interactions NBONDS: found 11442 intra-atom interactions NBONDS: found 11396 intra-atom interactions NBONDS: found 11436 intra-atom interactions NBONDS: found 11415 intra-atom interactions NBONDS: found 11405 intra-atom interactions NBONDS: found 11387 intra-atom interactions NBONDS: found 11392 intra-atom interactions NBONDS: found 11382 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=27458.519 E(kin)=6175.680 temperature=3060.309 | | Etotal =21282.839 grad(E)=68.438 E(BOND)=3009.418 E(ANGL)=4198.331 | | E(DIHE)=0.000 E(IMPR)=5373.894 E(VDW )=365.047 E(CDIH)=1363.026 | | E(NOE )=6807.117 E(PLAN)=166.007 | ------------------------------------------------------------------------------- NBONDS: found 11445 intra-atom interactions NBONDS: found 11556 intra-atom interactions NBONDS: found 11623 intra-atom interactions NBONDS: found 11686 intra-atom interactions NBONDS: found 11738 intra-atom interactions NBONDS: found 11776 intra-atom interactions NBONDS: found 11807 intra-atom interactions NBONDS: found 11892 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=27059.934 E(kin)=6027.806 temperature=2987.031 | | Etotal =21032.128 grad(E)=67.140 E(BOND)=2800.697 E(ANGL)=4396.016 | | E(DIHE)=0.000 E(IMPR)=5464.438 E(VDW )=430.703 E(CDIH)=1348.074 | | E(NOE )=6468.602 E(PLAN)=123.599 | ------------------------------------------------------------------------------- NBONDS: found 11917 intra-atom interactions NBONDS: found 11942 intra-atom interactions NBONDS: found 11948 intra-atom interactions NBONDS: found 11958 intra-atom interactions NBONDS: found 11975 intra-atom interactions CENMAS: Information about center of free masses position [A] : -0.00001 0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> constraints inter (all) (all) weights * 0.2 dihe 0.1 impr 0.1 vdw 20 end end SELRPN: 677 atoms have been selected out of 677 SELRPN: 677 atoms have been selected out of 677 X-PLOR> dynamics verlet DYNAmics> nstep=$nstep1 time=$high_timestep iasvel=current firstt=$init_t DYNAmics> tcoup=true tbath=$init_t nprint=100 iprfrq=0 DYNAmics> end DYNAMC: number of degrees of freedom= 2031 ASSVEL: current velocities taken. CENMAS: Information about center of free masses position [A] : -0.00001 0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : -0.00001 0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 728 exclusions and 0 interactions(1-4) NBONDS: found 11991 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=39884.106 E(kin)=6395.078 temperature=3169.030 | | Etotal =33489.028 grad(E)=137.626 E(BOND)=5502.731 E(ANGL)=9023.310 | | E(DIHE)=0.000 E(IMPR)=10665.961 E(VDW )=457.627 E(CDIH)=1270.648 | | E(NOE )=6464.356 E(PLAN)=104.395 | ------------------------------------------------------------------------------- NBONDS: found 12019 intra-atom interactions NBONDS: found 12017 intra-atom interactions NBONDS: found 12042 intra-atom interactions NBONDS: found 12037 intra-atom interactions NBONDS: found 12035 intra-atom interactions NBONDS: found 12055 intra-atom interactions NBONDS: found 12061 intra-atom interactions NBONDS: found 12092 intra-atom interactions NBONDS: found 12106 intra-atom interactions NBONDS: found 12108 intra-atom interactions NBONDS: found 12082 intra-atom interactions NBONDS: found 12064 intra-atom interactions NBONDS: found 12050 intra-atom interactions NBONDS: found 12070 intra-atom interactions NBONDS: found 12071 intra-atom interactions NBONDS: found 12043 intra-atom interactions NBONDS: found 12045 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=36791.955 E(kin)=7172.639 temperature=3554.344 | | Etotal =29619.316 grad(E)=94.126 E(BOND)=3453.302 E(ANGL)=6430.696 | | E(DIHE)=0.000 E(IMPR)=9281.310 E(VDW )=718.751 E(CDIH)=1761.515 | | E(NOE )=7843.695 E(PLAN)=130.048 | ------------------------------------------------------------------------------- NBONDS: found 12020 intra-atom interactions NBONDS: found 11990 intra-atom interactions NBONDS: found 12020 intra-atom interactions NBONDS: found 12017 intra-atom interactions NBONDS: found 11973 intra-atom interactions NBONDS: found 11923 intra-atom interactions NBONDS: found 11898 intra-atom interactions NBONDS: found 11851 intra-atom interactions NBONDS: found 11846 intra-atom interactions NBONDS: found 11793 intra-atom interactions NBONDS: found 11731 intra-atom interactions NBONDS: found 11693 intra-atom interactions NBONDS: found 11663 intra-atom interactions NBONDS: found 11660 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=34737.764 E(kin)=6235.173 temperature=3089.790 | | Etotal =28502.591 grad(E)=90.695 E(BOND)=3083.014 E(ANGL)=6386.814 | | E(DIHE)=0.000 E(IMPR)=8554.643 E(VDW )=490.486 E(CDIH)=1894.755 | | E(NOE )=7951.442 E(PLAN)=141.438 | ------------------------------------------------------------------------------- NBONDS: found 11666 intra-atom interactions NBONDS: found 11673 intra-atom interactions NBONDS: found 11655 intra-atom interactions NBONDS: found 11640 intra-atom interactions NBONDS: found 11650 intra-atom interactions NBONDS: found 11617 intra-atom interactions NBONDS: found 11595 intra-atom interactions NBONDS: found 11579 intra-atom interactions NBONDS: found 11498 intra-atom interactions NBONDS: found 11507 intra-atom interactions NBONDS: found 11466 intra-atom interactions NBONDS: found 11466 intra-atom interactions NBONDS: found 11476 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=34072.808 E(kin)=6177.151 temperature=3061.038 | | Etotal =27895.657 grad(E)=91.566 E(BOND)=3055.184 E(ANGL)=6192.461 | | E(DIHE)=0.000 E(IMPR)=8274.968 E(VDW )=431.695 E(CDIH)=1871.094 | | E(NOE )=7925.590 E(PLAN)=144.664 | ------------------------------------------------------------------------------- NBONDS: found 11516 intra-atom interactions NBONDS: found 11530 intra-atom interactions NBONDS: found 11530 intra-atom interactions NBONDS: found 11537 intra-atom interactions NBONDS: found 11502 intra-atom interactions NBONDS: found 11494 intra-atom interactions NBONDS: found 11449 intra-atom interactions NBONDS: found 11459 intra-atom interactions NBONDS: found 11528 intra-atom interactions NBONDS: found 11549 intra-atom interactions NBONDS: found 11562 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=33761.737 E(kin)=5966.314 temperature=2956.559 | | Etotal =27795.423 grad(E)=92.665 E(BOND)=3136.460 E(ANGL)=6154.308 | | E(DIHE)=0.000 E(IMPR)=8305.401 E(VDW )=522.677 E(CDIH)=1797.335 | | E(NOE )=7753.752 E(PLAN)=125.489 | ------------------------------------------------------------------------------- NBONDS: found 11618 intra-atom interactions NBONDS: found 11589 intra-atom interactions NBONDS: found 11630 intra-atom interactions NBONDS: found 11598 intra-atom interactions NBONDS: found 11621 intra-atom interactions NBONDS: found 11655 intra-atom interactions NBONDS: found 11642 intra-atom interactions NBONDS: found 11698 intra-atom interactions NBONDS: found 11711 intra-atom interactions NBONDS: found 11720 intra-atom interactions NBONDS: found 11694 intra-atom interactions NBONDS: found 11700 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=33094.438 E(kin)=6574.497 temperature=3257.939 | | Etotal =26519.941 grad(E)=89.416 E(BOND)=2695.511 E(ANGL)=6419.489 | | E(DIHE)=0.000 E(IMPR)=7799.154 E(VDW )=403.710 E(CDIH)=1747.078 | | E(NOE )=7251.558 E(PLAN)=203.441 | ------------------------------------------------------------------------------- NBONDS: found 11710 intra-atom interactions NBONDS: found 11787 intra-atom interactions NBONDS: found 11798 intra-atom interactions NBONDS: found 11725 intra-atom interactions NBONDS: found 11755 intra-atom interactions NBONDS: found 11749 intra-atom interactions NBONDS: found 11751 intra-atom interactions NBONDS: found 11757 intra-atom interactions NBONDS: found 11758 intra-atom interactions NBONDS: found 11736 intra-atom interactions NBONDS: found 11698 intra-atom interactions NBONDS: found 11700 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=34443.386 E(kin)=7412.926 temperature=3673.416 | | Etotal =27030.460 grad(E)=90.675 E(BOND)=2975.509 E(ANGL)=6068.179 | | E(DIHE)=0.000 E(IMPR)=8398.058 E(VDW )=575.749 E(CDIH)=1660.321 | | E(NOE )=7175.055 E(PLAN)=177.590 | ------------------------------------------------------------------------------- NBONDS: found 11705 intra-atom interactions NBONDS: found 11709 intra-atom interactions NBONDS: found 11761 intra-atom interactions NBONDS: found 11783 intra-atom interactions NBONDS: found 11791 intra-atom interactions NBONDS: found 11767 intra-atom interactions NBONDS: found 11753 intra-atom interactions NBONDS: found 11754 intra-atom interactions NBONDS: found 11736 intra-atom interactions NBONDS: found 11731 intra-atom interactions NBONDS: found 11753 intra-atom interactions NBONDS: found 11749 intra-atom interactions NBONDS: found 11749 intra-atom interactions NBONDS: found 11714 intra-atom interactions NBONDS: found 11690 intra-atom interactions NBONDS: found 11663 intra-atom interactions NBONDS: found 11644 intra-atom interactions NBONDS: found 11655 intra-atom interactions NBONDS: found 11631 intra-atom interactions NBONDS: found 11641 intra-atom interactions NBONDS: found 11660 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=34492.259 E(kin)=7117.125 temperature=3526.834 | | Etotal =27375.135 grad(E)=100.025 E(BOND)=3576.057 E(ANGL)=6061.956 | | E(DIHE)=0.000 E(IMPR)=8278.173 E(VDW )=677.278 E(CDIH)=1766.796 | | E(NOE )=6769.255 E(PLAN)=245.619 | ------------------------------------------------------------------------------- NBONDS: found 11625 intra-atom interactions NBONDS: found 11620 intra-atom interactions NBONDS: found 11592 intra-atom interactions NBONDS: found 11599 intra-atom interactions NBONDS: found 11584 intra-atom interactions NBONDS: found 11599 intra-atom interactions NBONDS: found 11638 intra-atom interactions NBONDS: found 11631 intra-atom interactions CENMAS: Information about center of free masses position [A] : -0.00001 0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> constraints inter (all) (all) weights * 0.2 dihe 0.2 impr 0.2 vdw 0.01 end end SELRPN: 677 atoms have been selected out of 677 SELRPN: 677 atoms have been selected out of 677 X-PLOR> parameter nbonds repel=0.9 end end X-PLOR> dynamics verlet DYNAmics> nstep=$nstep1 time=$high_timestep iasvel=current firstt=$init_t DYNAmics> tcoup=true tbath=$init_t nprint=100 iprfrq=0 DYNAmics> end DYNAMC: number of degrees of freedom= 2031 ASSVEL: current velocities taken. CENMAS: Information about center of free masses position [A] : -0.00001 0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : -0.00001 0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 CODBON: bond type-based parameters retrieved CODANG: angle type-based parameters retrieved CODIMP: improper type-based parameters retrieved NBUPDA: type-based van der Waals parameters retrieved. NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 728 exclusions and 0 interactions(1-4) NBONDS: found 11637 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=40993.710 E(kin)=5930.923 temperature=2939.021 | | Etotal =35062.787 grad(E)=130.113 E(BOND)=2966.422 E(ANGL)=6160.700 | | E(DIHE)=0.000 E(IMPR)=16206.097 E(VDW )=342.191 E(CDIH)=1689.340 | | E(NOE )=7490.352 E(PLAN)=207.684 | ------------------------------------------------------------------------------- NBONDS: found 11653 intra-atom interactions NBONDS: found 11610 intra-atom interactions NBONDS: found 11616 intra-atom interactions NBONDS: found 11631 intra-atom interactions NBONDS: found 11684 intra-atom interactions NBONDS: found 11742 intra-atom interactions NBONDS: found 11856 intra-atom interactions NBONDS: found 11918 intra-atom interactions NBONDS: found 11968 intra-atom interactions NBONDS: found 12033 intra-atom interactions NBONDS: found 12087 intra-atom interactions NBONDS: found 12143 intra-atom interactions NBONDS: found 12224 intra-atom interactions NBONDS: found 12265 intra-atom interactions NBONDS: found 12330 intra-atom interactions NBONDS: found 12376 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=34673.183 E(kin)=8481.314 temperature=4202.847 | | Etotal =26191.869 grad(E)=103.756 E(BOND)=3630.867 E(ANGL)=8786.993 | | E(DIHE)=0.000 E(IMPR)=3258.118 E(VDW )=435.273 E(CDIH)=1807.155 | | E(NOE )=8086.312 E(PLAN)=187.150 | ------------------------------------------------------------------------------- NBONDS: found 12374 intra-atom interactions NBONDS: found 12416 intra-atom interactions NBONDS: found 12411 intra-atom interactions NBONDS: found 12446 intra-atom interactions NBONDS: found 12474 intra-atom interactions NBONDS: found 12464 intra-atom interactions NBONDS: found 12486 intra-atom interactions NBONDS: found 12572 intra-atom interactions NBONDS: found 12621 intra-atom interactions NBONDS: found 12718 intra-atom interactions NBONDS: found 12744 intra-atom interactions NBONDS: found 12744 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=29592.837 E(kin)=6966.586 temperature=3452.236 | | Etotal =22626.252 grad(E)=94.867 E(BOND)=3587.400 E(ANGL)=7389.778 | | E(DIHE)=0.000 E(IMPR)=1921.664 E(VDW )=478.720 E(CDIH)=1741.199 | | E(NOE )=7246.989 E(PLAN)=260.502 | ------------------------------------------------------------------------------- NBONDS: found 12812 intra-atom interactions NBONDS: found 12923 intra-atom interactions NBONDS: found 12935 intra-atom interactions NBONDS: found 12949 intra-atom interactions NBONDS: found 12996 intra-atom interactions NBONDS: found 12963 intra-atom interactions NBONDS: found 12992 intra-atom interactions NBONDS: found 12986 intra-atom interactions NBONDS: found 12995 intra-atom interactions NBONDS: found 12997 intra-atom interactions NBONDS: found 12992 intra-atom interactions NBONDS: found 12998 intra-atom interactions NBONDS: found 12999 intra-atom interactions NBONDS: found 13000 intra-atom interactions NBONDS: found 13003 intra-atom interactions NBONDS: found 13011 intra-atom interactions NBONDS: found 13027 intra-atom interactions NBONDS: found 12997 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=40952.418 E(kin)=13300.439 temperature=6590.926 | | Etotal =27651.979 grad(E)=150.053 E(BOND)=7384.911 E(ANGL)=6710.224 | | E(DIHE)=0.000 E(IMPR)=3353.855 E(VDW )=467.692 E(CDIH)=1737.089 | | E(NOE )=7781.548 E(PLAN)=216.660 | ------------------------------------------------------------------------------- NBONDS: found 12999 intra-atom interactions NBONDS: found 12984 intra-atom interactions NBONDS: found 12987 intra-atom interactions NBONDS: found 12998 intra-atom interactions NBONDS: found 13004 intra-atom interactions NBONDS: found 13015 intra-atom interactions NBONDS: found 13034 intra-atom interactions NBONDS: found 13044 intra-atom interactions NBONDS: found 13045 intra-atom interactions NBONDS: found 13060 intra-atom interactions NBONDS: found 13096 intra-atom interactions NBONDS: found 13074 intra-atom interactions NBONDS: found 13108 intra-atom interactions NBONDS: found 13137 intra-atom interactions NBONDS: found 13163 intra-atom interactions NBONDS: found 13165 intra-atom interactions NBONDS: found 13165 intra-atom interactions NBONDS: found 13186 intra-atom interactions NBONDS: found 13188 intra-atom interactions NBONDS: found 13228 intra-atom interactions NBONDS: found 13266 intra-atom interactions NBONDS: found 13280 intra-atom interactions NBONDS: found 13277 intra-atom interactions NBONDS: found 13282 intra-atom interactions NBONDS: found 13307 intra-atom interactions NBONDS: found 13314 intra-atom interactions NBONDS: found 13357 intra-atom interactions NBONDS: found 13374 intra-atom interactions NBONDS: found 13416 intra-atom interactions NBONDS: found 13454 intra-atom interactions NBONDS: found 13441 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=31962.496 E(kin)=8447.531 temperature=4186.106 | | Etotal =23514.965 grad(E)=120.125 E(BOND)=4436.123 E(ANGL)=7072.810 | | E(DIHE)=0.000 E(IMPR)=2277.904 E(VDW )=492.243 E(CDIH)=1289.432 | | E(NOE )=7695.432 E(PLAN)=251.021 | ------------------------------------------------------------------------------- NBONDS: found 13456 intra-atom interactions NBONDS: found 13494 intra-atom interactions NBONDS: found 13531 intra-atom interactions NBONDS: found 13535 intra-atom interactions NBONDS: found 13567 intra-atom interactions NBONDS: found 13557 intra-atom interactions NBONDS: found 13578 intra-atom interactions NBONDS: found 13572 intra-atom interactions NBONDS: found 13598 intra-atom interactions NBONDS: found 13607 intra-atom interactions NBONDS: found 13629 intra-atom interactions NBONDS: found 13643 intra-atom interactions NBONDS: found 13645 intra-atom interactions NBONDS: found 13658 intra-atom interactions NBONDS: found 13687 intra-atom interactions NBONDS: found 13679 intra-atom interactions NBONDS: found 13672 intra-atom interactions NBONDS: found 13678 intra-atom interactions NBONDS: found 13694 intra-atom interactions NBONDS: found 13719 intra-atom interactions NBONDS: found 13686 intra-atom interactions NBONDS: found 13666 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=27985.260 E(kin)=6599.209 temperature=3270.185 | | Etotal =21386.051 grad(E)=122.289 E(BOND)=3575.835 E(ANGL)=6147.932 | | E(DIHE)=0.000 E(IMPR)=2333.522 E(VDW )=494.192 E(CDIH)=1117.929 | | E(NOE )=7422.954 E(PLAN)=293.687 | ------------------------------------------------------------------------------- NBONDS: found 13680 intra-atom interactions NBONDS: found 13706 intra-atom interactions NBONDS: found 13673 intra-atom interactions NBONDS: found 13669 intra-atom interactions NBONDS: found 13647 intra-atom interactions NBONDS: found 13662 intra-atom interactions NBONDS: found 13684 intra-atom interactions NBONDS: found 13680 intra-atom interactions NBONDS: found 13702 intra-atom interactions NBONDS: found 13709 intra-atom interactions NBONDS: found 13708 intra-atom interactions NBONDS: found 13756 intra-atom interactions NBONDS: found 13735 intra-atom interactions NBONDS: found 13710 intra-atom interactions NBONDS: found 13691 intra-atom interactions NBONDS: found 13656 intra-atom interactions NBONDS: found 13645 intra-atom interactions NBONDS: found 13643 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=28432.716 E(kin)=6503.981 temperature=3222.996 | | Etotal =21928.735 grad(E)=147.194 E(BOND)=3316.452 E(ANGL)=5757.013 | | E(DIHE)=0.000 E(IMPR)=3207.980 E(VDW )=492.114 E(CDIH)=1469.759 | | E(NOE )=7466.569 E(PLAN)=218.846 | ------------------------------------------------------------------------------- NBONDS: found 13660 intra-atom interactions NBONDS: found 13648 intra-atom interactions NBONDS: found 13623 intra-atom interactions NBONDS: found 13623 intra-atom interactions NBONDS: found 13603 intra-atom interactions NBONDS: found 13644 intra-atom interactions NBONDS: found 13676 intra-atom interactions NBONDS: found 13672 intra-atom interactions NBONDS: found 13673 intra-atom interactions NBONDS: found 13670 intra-atom interactions NBONDS: found 13676 intra-atom interactions NBONDS: found 13655 intra-atom interactions NBONDS: found 13693 intra-atom interactions NBONDS: found 13726 intra-atom interactions NBONDS: found 13731 intra-atom interactions NBONDS: found 13731 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=27474.212 E(kin)=6435.858 temperature=3189.238 | | Etotal =21038.354 grad(E)=108.072 E(BOND)=3282.486 E(ANGL)=5865.494 | | E(DIHE)=0.000 E(IMPR)=2366.592 E(VDW )=500.309 E(CDIH)=1273.005 | | E(NOE )=7492.102 E(PLAN)=258.366 | ------------------------------------------------------------------------------- NBONDS: found 13726 intra-atom interactions NBONDS: found 13700 intra-atom interactions NBONDS: found 13691 intra-atom interactions NBONDS: found 13694 intra-atom interactions NBONDS: found 13746 intra-atom interactions NBONDS: found 13802 intra-atom interactions NBONDS: found 13808 intra-atom interactions NBONDS: found 13808 intra-atom interactions CENMAS: Information about center of free masses position [A] : -0.00001 0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> constraints inter (all) (all) weights * 0.4 dihe 0.4 impr 0.4 vdw 0.003 end end SELRPN: 677 atoms have been selected out of 677 SELRPN: 677 atoms have been selected out of 677 X-PLOR> parameter nbonds nbxmod=-3 end end X-PLOR> dynamics verlet DYNAmics> nstep=$nstep2 time=$high_timestep iasvel=current firstt=$init_t DYNAmics> tcoup=true tbath=$init_t nprint=100 iprfrq=0 DYNAmics> end DYNAMC: number of degrees of freedom= 2031 ASSVEL: current velocities taken. CENMAS: Information about center of free masses position [A] : -0.00001 0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : -0.00001 0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 CODBON: bond type-based parameters retrieved CODANG: angle type-based parameters retrieved CODIMP: improper type-based parameters retrieved NBUPDA: type-based van der Waals parameters retrieved. NBONDS: generating intra-molecular exclusion list with mode=-3 MAKINB: mode -3 found 2027 exclusions and 0 interactions(1-4) NBONDS: found 12514 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=38232.227 E(kin)=6265.002 temperature=3104.572 | | Etotal =31967.225 grad(E)=216.523 E(BOND)=6890.369 E(ANGL)=12163.344 | | E(DIHE)=0.000 E(IMPR)=3877.190 E(VDW )=95.340 E(CDIH)=1230.404 | | E(NOE )=7481.805 E(PLAN)=228.773 | ------------------------------------------------------------------------------- NBONDS: found 12508 intra-atom interactions NBONDS: found 12567 intra-atom interactions NBONDS: found 12617 intra-atom interactions NBONDS: found 12692 intra-atom interactions NBONDS: found 12750 intra-atom interactions NBONDS: found 12794 intra-atom interactions NBONDS: found 12850 intra-atom interactions NBONDS: found 12866 intra-atom interactions NBONDS: found 12895 intra-atom interactions NBONDS: found 12986 intra-atom interactions NBONDS: found 13016 intra-atom interactions NBONDS: found 13080 intra-atom interactions NBONDS: found 13137 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=32876.488 E(kin)=6969.318 temperature=3453.590 | | Etotal =25907.171 grad(E)=166.199 E(BOND)=3767.155 E(ANGL)=7884.647 | | E(DIHE)=0.000 E(IMPR)=2233.593 E(VDW )=103.199 E(CDIH)=1586.162 | | E(NOE )=10020.475 E(PLAN)=311.940 | ------------------------------------------------------------------------------- NBONDS: found 13148 intra-atom interactions NBONDS: found 13120 intra-atom interactions NBONDS: found 13131 intra-atom interactions NBONDS: found 13169 intra-atom interactions NBONDS: found 13211 intra-atom interactions NBONDS: found 13211 intra-atom interactions NBONDS: found 13231 intra-atom interactions NBONDS: found 13239 intra-atom interactions NBONDS: found 13287 intra-atom interactions NBONDS: found 13315 intra-atom interactions NBONDS: found 13317 intra-atom interactions NBONDS: found 13356 intra-atom interactions NBONDS: found 13318 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=31395.801 E(kin)=6115.479 temperature=3030.477 | | Etotal =25280.322 grad(E)=158.348 E(BOND)=3611.662 E(ANGL)=7627.730 | | E(DIHE)=0.000 E(IMPR)=2024.324 E(VDW )=105.763 E(CDIH)=1599.939 | | E(NOE )=10039.868 E(PLAN)=271.035 | ------------------------------------------------------------------------------- NBONDS: found 13349 intra-atom interactions NBONDS: found 13364 intra-atom interactions NBONDS: found 13385 intra-atom interactions NBONDS: found 13383 intra-atom interactions NBONDS: found 13371 intra-atom interactions NBONDS: found 13353 intra-atom interactions NBONDS: found 13367 intra-atom interactions NBONDS: found 13387 intra-atom interactions NBONDS: found 13405 intra-atom interactions NBONDS: found 13405 intra-atom interactions NBONDS: found 13377 intra-atom interactions NBONDS: found 13412 intra-atom interactions NBONDS: found 13455 intra-atom interactions NBONDS: found 13497 intra-atom interactions NBONDS: found 13529 intra-atom interactions NBONDS: found 13524 intra-atom interactions NBONDS: found 13555 intra-atom interactions NBONDS: found 13571 intra-atom interactions NBONDS: found 13628 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=31617.616 E(kin)=6125.652 temperature=3035.518 | | Etotal =25491.964 grad(E)=163.467 E(BOND)=3842.588 E(ANGL)=7558.193 | | E(DIHE)=0.000 E(IMPR)=1744.538 E(VDW )=109.245 E(CDIH)=1560.816 | | E(NOE )=10440.749 E(PLAN)=235.835 | ------------------------------------------------------------------------------- NBONDS: found 13689 intra-atom interactions NBONDS: found 13725 intra-atom interactions NBONDS: found 13746 intra-atom interactions NBONDS: found 13782 intra-atom interactions NBONDS: found 13820 intra-atom interactions NBONDS: found 13840 intra-atom interactions NBONDS: found 13890 intra-atom interactions NBONDS: found 13910 intra-atom interactions NBONDS: found 13926 intra-atom interactions NBONDS: found 13943 intra-atom interactions NBONDS: found 13892 intra-atom interactions NBONDS: found 13901 intra-atom interactions NBONDS: found 13900 intra-atom interactions NBONDS: found 13904 intra-atom interactions NBONDS: found 13867 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=31427.012 E(kin)=6314.263 temperature=3128.982 | | Etotal =25112.750 grad(E)=146.922 E(BOND)=3312.737 E(ANGL)=7493.991 | | E(DIHE)=0.000 E(IMPR)=2063.682 E(VDW )=116.603 E(CDIH)=1536.687 | | E(NOE )=10305.810 E(PLAN)=283.239 | ------------------------------------------------------------------------------- NBONDS: found 13874 intra-atom interactions NBONDS: found 13889 intra-atom interactions NBONDS: found 13898 intra-atom interactions NBONDS: found 13916 intra-atom interactions NBONDS: found 13924 intra-atom interactions NBONDS: found 13932 intra-atom interactions NBONDS: found 13929 intra-atom interactions NBONDS: found 13971 intra-atom interactions NBONDS: found 14022 intra-atom interactions NBONDS: found 14040 intra-atom interactions NBONDS: found 14048 intra-atom interactions NBONDS: found 14065 intra-atom interactions NBONDS: found 14125 intra-atom interactions NBONDS: found 14108 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=31039.589 E(kin)=5839.110 temperature=2893.524 | | Etotal =25200.479 grad(E)=149.157 E(BOND)=3323.136 E(ANGL)=8607.188 | | E(DIHE)=0.000 E(IMPR)=1748.974 E(VDW )=118.397 E(CDIH)=1749.054 | | E(NOE )=9312.228 E(PLAN)=341.502 | ------------------------------------------------------------------------------- NBONDS: found 14112 intra-atom interactions NBONDS: found 14093 intra-atom interactions NBONDS: found 14074 intra-atom interactions NBONDS: found 14055 intra-atom interactions NBONDS: found 14038 intra-atom interactions NBONDS: found 14059 intra-atom interactions NBONDS: found 14083 intra-atom interactions NBONDS: found 14123 intra-atom interactions NBONDS: found 14130 intra-atom interactions NBONDS: found 14141 intra-atom interactions NBONDS: found 14194 intra-atom interactions NBONDS: found 14180 intra-atom interactions NBONDS: found 14146 intra-atom interactions NBONDS: found 14183 intra-atom interactions NBONDS: found 14209 intra-atom interactions NBONDS: found 14230 intra-atom interactions NBONDS: found 14282 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=31154.437 E(kin)=6840.754 temperature=3389.881 | | Etotal =24313.684 grad(E)=133.998 E(BOND)=3119.198 E(ANGL)=7681.561 | | E(DIHE)=0.000 E(IMPR)=1834.484 E(VDW )=122.654 E(CDIH)=1610.854 | | E(NOE )=9650.129 E(PLAN)=294.803 | ------------------------------------------------------------------------------- NBONDS: found 14355 intra-atom interactions NBONDS: found 14412 intra-atom interactions NBONDS: found 14448 intra-atom interactions NBONDS: found 14450 intra-atom interactions NBONDS: found 14485 intra-atom interactions NBONDS: found 14509 intra-atom interactions NBONDS: found 14524 intra-atom interactions NBONDS: found 14580 intra-atom interactions NBONDS: found 14613 intra-atom interactions NBONDS: found 14615 intra-atom interactions NBONDS: found 14601 intra-atom interactions NBONDS: found 14624 intra-atom interactions NBONDS: found 14633 intra-atom interactions NBONDS: found 14622 intra-atom interactions NBONDS: found 14634 intra-atom interactions NBONDS: found 14675 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=31319.650 E(kin)=6373.329 temperature=3158.252 | | Etotal =24946.321 grad(E)=143.167 E(BOND)=3197.154 E(ANGL)=8270.463 | | E(DIHE)=0.000 E(IMPR)=1781.702 E(VDW )=132.663 E(CDIH)=1532.003 | | E(NOE )=9680.127 E(PLAN)=352.208 | ------------------------------------------------------------------------------- NBONDS: found 14730 intra-atom interactions NBONDS: found 14796 intra-atom interactions NBONDS: found 14837 intra-atom interactions NBONDS: found 14874 intra-atom interactions NBONDS: found 14931 intra-atom interactions NBONDS: found 14947 intra-atom interactions NBONDS: found 14953 intra-atom interactions NBONDS: found 14995 intra-atom interactions NBONDS: found 14982 intra-atom interactions NBONDS: found 14941 intra-atom interactions NBONDS: found 14977 intra-atom interactions NBONDS: found 14986 intra-atom interactions NBONDS: found 15005 intra-atom interactions NBONDS: found 15007 intra-atom interactions NBONDS: found 15022 intra-atom interactions NBONDS: found 15023 intra-atom interactions --------------- step= 800 at 1.60000 ps -------------------------------- | E(kin)+E(total)=31676.668 E(kin)=6371.234 temperature=3157.214 | | Etotal =25305.435 grad(E)=137.652 E(BOND)=3530.205 E(ANGL)=7815.073 | | E(DIHE)=0.000 E(IMPR)=2245.713 E(VDW )=142.203 E(CDIH)=1763.578 | | E(NOE )=9516.642 E(PLAN)=292.021 | ------------------------------------------------------------------------------- NBONDS: found 15053 intra-atom interactions NBONDS: found 15081 intra-atom interactions NBONDS: found 15101 intra-atom interactions NBONDS: found 15108 intra-atom interactions NBONDS: found 15118 intra-atom interactions NBONDS: found 15171 intra-atom interactions NBONDS: found 15202 intra-atom interactions NBONDS: found 15236 intra-atom interactions NBONDS: found 15296 intra-atom interactions NBONDS: found 15345 intra-atom interactions NBONDS: found 15339 intra-atom interactions NBONDS: found 15361 intra-atom interactions NBONDS: found 15361 intra-atom interactions NBONDS: found 15345 intra-atom interactions --------------- step= 900 at 1.80000 ps -------------------------------- | E(kin)+E(total)=31635.127 E(kin)=6823.602 temperature=3381.381 | | Etotal =24811.525 grad(E)=134.102 E(BOND)=3108.170 E(ANGL)=7441.595 | | E(DIHE)=0.000 E(IMPR)=1887.088 E(VDW )=145.344 E(CDIH)=1729.342 | | E(NOE )=10194.705 E(PLAN)=305.280 | ------------------------------------------------------------------------------- NBONDS: found 15303 intra-atom interactions NBONDS: found 15291 intra-atom interactions NBONDS: found 15250 intra-atom interactions NBONDS: found 15257 intra-atom interactions NBONDS: found 15239 intra-atom interactions NBONDS: found 15241 intra-atom interactions NBONDS: found 15227 intra-atom interactions NBONDS: found 15180 intra-atom interactions NBONDS: found 15177 intra-atom interactions NBONDS: found 15206 intra-atom interactions NBONDS: found 15147 intra-atom interactions NBONDS: found 15110 intra-atom interactions NBONDS: found 15145 intra-atom interactions NBONDS: found 15071 intra-atom interactions NBONDS: found 15069 intra-atom interactions --------------- step= 1000 at 2.00000 ps -------------------------------- | E(kin)+E(total)=31197.131 E(kin)=6333.396 temperature=3138.463 | | Etotal =24863.735 grad(E)=142.410 E(BOND)=3732.360 E(ANGL)=7533.339 | | E(DIHE)=0.000 E(IMPR)=1767.414 E(VDW )=141.515 E(CDIH)=1580.301 | | E(NOE )=9780.135 E(PLAN)=328.670 | ------------------------------------------------------------------------------- NBONDS: found 15071 intra-atom interactions NBONDS: found 15095 intra-atom interactions NBONDS: found 15126 intra-atom interactions NBONDS: found 15152 intra-atom interactions NBONDS: found 15169 intra-atom interactions NBONDS: found 15155 intra-atom interactions NBONDS: found 15144 intra-atom interactions NBONDS: found 15141 intra-atom interactions NBONDS: found 15195 intra-atom interactions NBONDS: found 15178 intra-atom interactions NBONDS: found 15207 intra-atom interactions NBONDS: found 15241 intra-atom interactions NBONDS: found 15258 intra-atom interactions NBONDS: found 15259 intra-atom interactions NBONDS: found 15252 intra-atom interactions NBONDS: found 15259 intra-atom interactions --------------- step= 1100 at 2.20000 ps -------------------------------- | E(kin)+E(total)=31685.087 E(kin)=6637.739 temperature=3289.278 | | Etotal =25047.347 grad(E)=145.153 E(BOND)=3142.667 E(ANGL)=7406.429 | | E(DIHE)=0.000 E(IMPR)=2126.965 E(VDW )=146.086 E(CDIH)=1638.590 | | E(NOE )=10252.830 E(PLAN)=333.780 | ------------------------------------------------------------------------------- NBONDS: found 15246 intra-atom interactions NBONDS: found 15249 intra-atom interactions NBONDS: found 15230 intra-atom interactions NBONDS: found 15218 intra-atom interactions NBONDS: found 15180 intra-atom interactions NBONDS: found 15172 intra-atom interactions NBONDS: found 15173 intra-atom interactions NBONDS: found 15219 intra-atom interactions NBONDS: found 15190 intra-atom interactions NBONDS: found 15150 intra-atom interactions NBONDS: found 15133 intra-atom interactions NBONDS: found 15163 intra-atom interactions NBONDS: found 15151 intra-atom interactions NBONDS: found 15169 intra-atom interactions NBONDS: found 15192 intra-atom interactions NBONDS: found 15205 intra-atom interactions NBONDS: found 15192 intra-atom interactions NBONDS: found 15194 intra-atom interactions --------------- step= 1200 at 2.40000 ps -------------------------------- | E(kin)+E(total)=32252.159 E(kin)=6674.689 temperature=3307.588 | | Etotal =25577.470 grad(E)=154.463 E(BOND)=3633.124 E(ANGL)=7616.965 | | E(DIHE)=0.000 E(IMPR)=2005.526 E(VDW )=141.120 E(CDIH)=1748.985 | | E(NOE )=10111.121 E(PLAN)=320.629 | ------------------------------------------------------------------------------- NBONDS: found 15229 intra-atom interactions NBONDS: found 15254 intra-atom interactions NBONDS: found 15245 intra-atom interactions NBONDS: found 15218 intra-atom interactions NBONDS: found 15189 intra-atom interactions NBONDS: found 15189 intra-atom interactions NBONDS: found 15170 intra-atom interactions NBONDS: found 15109 intra-atom interactions NBONDS: found 15095 intra-atom interactions NBONDS: found 15075 intra-atom interactions NBONDS: found 15073 intra-atom interactions NBONDS: found 15062 intra-atom interactions NBONDS: found 15041 intra-atom interactions NBONDS: found 15038 intra-atom interactions NBONDS: found 15093 intra-atom interactions NBONDS: found 15121 intra-atom interactions NBONDS: found 15152 intra-atom interactions --------------- step= 1300 at 2.60000 ps -------------------------------- | E(kin)+E(total)=31100.199 E(kin)=6388.485 temperature=3165.762 | | Etotal =24711.714 grad(E)=143.284 E(BOND)=2986.352 E(ANGL)=7260.365 | | E(DIHE)=0.000 E(IMPR)=2178.826 E(VDW )=140.814 E(CDIH)=1727.644 | | E(NOE )=10079.626 E(PLAN)=338.087 | ------------------------------------------------------------------------------- NBONDS: found 15172 intra-atom interactions NBONDS: found 15198 intra-atom interactions NBONDS: found 15202 intra-atom interactions NBONDS: found 15187 intra-atom interactions NBONDS: found 15207 intra-atom interactions NBONDS: found 15160 intra-atom interactions NBONDS: found 15142 intra-atom interactions NBONDS: found 15152 intra-atom interactions NBONDS: found 15170 intra-atom interactions NBONDS: found 15130 intra-atom interactions NBONDS: found 15139 intra-atom interactions NBONDS: found 15150 intra-atom interactions NBONDS: found 15112 intra-atom interactions NBONDS: found 15080 intra-atom interactions NBONDS: found 15059 intra-atom interactions --------------- step= 1400 at 2.80000 ps -------------------------------- | E(kin)+E(total)=31235.111 E(kin)=6530.233 temperature=3236.005 | | Etotal =24704.877 grad(E)=134.776 E(BOND)=3424.670 E(ANGL)=8025.498 | | E(DIHE)=0.000 E(IMPR)=1737.381 E(VDW )=139.451 E(CDIH)=1696.474 | | E(NOE )=9409.081 E(PLAN)=272.321 | ------------------------------------------------------------------------------- NBONDS: found 15050 intra-atom interactions NBONDS: found 14994 intra-atom interactions NBONDS: found 14980 intra-atom interactions NBONDS: found 14968 intra-atom interactions NBONDS: found 14904 intra-atom interactions NBONDS: found 14910 intra-atom interactions NBONDS: found 14886 intra-atom interactions NBONDS: found 14837 intra-atom interactions NBONDS: found 14812 intra-atom interactions NBONDS: found 14803 intra-atom interactions NBONDS: found 14801 intra-atom interactions NBONDS: found 14724 intra-atom interactions NBONDS: found 14687 intra-atom interactions NBONDS: found 14725 intra-atom interactions NBONDS: found 14696 intra-atom interactions NBONDS: found 14698 intra-atom interactions NBONDS: found 14678 intra-atom interactions --------------- step= 1500 at 3.00000 ps -------------------------------- | E(kin)+E(total)=30980.627 E(kin)=6121.598 temperature=3033.509 | | Etotal =24859.029 grad(E)=137.712 E(BOND)=3513.736 E(ANGL)=7450.520 | | E(DIHE)=0.000 E(IMPR)=1934.867 E(VDW )=130.416 E(CDIH)=1809.146 | | E(NOE )=9777.999 E(PLAN)=242.345 | ------------------------------------------------------------------------------- NBONDS: found 14668 intra-atom interactions NBONDS: found 14594 intra-atom interactions NBONDS: found 14550 intra-atom interactions NBONDS: found 14499 intra-atom interactions NBONDS: found 14426 intra-atom interactions NBONDS: found 14412 intra-atom interactions NBONDS: found 14374 intra-atom interactions NBONDS: found 14338 intra-atom interactions NBONDS: found 14344 intra-atom interactions NBONDS: found 14320 intra-atom interactions NBONDS: found 14316 intra-atom interactions NBONDS: found 14315 intra-atom interactions NBONDS: found 14307 intra-atom interactions NBONDS: found 14284 intra-atom interactions NBONDS: found 14271 intra-atom interactions NBONDS: found 14253 intra-atom interactions NBONDS: found 14262 intra-atom interactions --------------- step= 1600 at 3.20000 ps -------------------------------- | E(kin)+E(total)=32030.796 E(kin)=6870.464 temperature=3404.604 | | Etotal =25160.332 grad(E)=152.619 E(BOND)=3639.502 E(ANGL)=8048.004 | | E(DIHE)=0.000 E(IMPR)=1681.497 E(VDW )=118.035 E(CDIH)=1574.894 | | E(NOE )=9812.898 E(PLAN)=285.502 | ------------------------------------------------------------------------------- NBONDS: found 14270 intra-atom interactions NBONDS: found 14271 intra-atom interactions NBONDS: found 14261 intra-atom interactions NBONDS: found 14231 intra-atom interactions NBONDS: found 14204 intra-atom interactions NBONDS: found 14161 intra-atom interactions NBONDS: found 14150 intra-atom interactions NBONDS: found 14131 intra-atom interactions NBONDS: found 14127 intra-atom interactions NBONDS: found 14077 intra-atom interactions NBONDS: found 14047 intra-atom interactions NBONDS: found 14032 intra-atom interactions NBONDS: found 14028 intra-atom interactions NBONDS: found 14024 intra-atom interactions NBONDS: found 14026 intra-atom interactions NBONDS: found 14034 intra-atom interactions --------------- step= 1700 at 3.40000 ps -------------------------------- | E(kin)+E(total)=31113.797 E(kin)=6339.955 temperature=3141.714 | | Etotal =24773.843 grad(E)=146.195 E(BOND)=3334.713 E(ANGL)=8043.275 | | E(DIHE)=0.000 E(IMPR)=1896.060 E(VDW )=115.068 E(CDIH)=1378.817 | | E(NOE )=9756.947 E(PLAN)=248.961 | ------------------------------------------------------------------------------- NBONDS: found 14062 intra-atom interactions NBONDS: found 14027 intra-atom interactions NBONDS: found 14025 intra-atom interactions NBONDS: found 14060 intra-atom interactions NBONDS: found 14040 intra-atom interactions NBONDS: found 14049 intra-atom interactions NBONDS: found 14059 intra-atom interactions NBONDS: found 14042 intra-atom interactions NBONDS: found 14043 intra-atom interactions NBONDS: found 14047 intra-atom interactions NBONDS: found 14014 intra-atom interactions NBONDS: found 14001 intra-atom interactions NBONDS: found 14000 intra-atom interactions NBONDS: found 13969 intra-atom interactions NBONDS: found 13954 intra-atom interactions NBONDS: found 13912 intra-atom interactions NBONDS: found 13920 intra-atom interactions --------------- step= 1800 at 3.60000 ps -------------------------------- | E(kin)+E(total)=30800.141 E(kin)=6039.128 temperature=2992.642 | | Etotal =24761.013 grad(E)=152.951 E(BOND)=3617.144 E(ANGL)=7701.255 | | E(DIHE)=0.000 E(IMPR)=1839.096 E(VDW )=113.933 E(CDIH)=1703.001 | | E(NOE )=9490.163 E(PLAN)=296.422 | ------------------------------------------------------------------------------- NBONDS: found 13891 intra-atom interactions NBONDS: found 13915 intra-atom interactions NBONDS: found 13931 intra-atom interactions NBONDS: found 13885 intra-atom interactions NBONDS: found 13875 intra-atom interactions NBONDS: found 13894 intra-atom interactions NBONDS: found 13888 intra-atom interactions NBONDS: found 13890 intra-atom interactions NBONDS: found 13888 intra-atom interactions NBONDS: found 13926 intra-atom interactions NBONDS: found 13923 intra-atom interactions NBONDS: found 13925 intra-atom interactions NBONDS: found 13944 intra-atom interactions NBONDS: found 13932 intra-atom interactions NBONDS: found 13886 intra-atom interactions NBONDS: found 13886 intra-atom interactions NBONDS: found 13891 intra-atom interactions NBONDS: found 13889 intra-atom interactions NBONDS: found 13868 intra-atom interactions NBONDS: found 13867 intra-atom interactions NBONDS: found 13868 intra-atom interactions NBONDS: found 13867 intra-atom interactions NBONDS: found 13854 intra-atom interactions NBONDS: found 13864 intra-atom interactions --------------- step= 1900 at 3.80000 ps -------------------------------- | E(kin)+E(total)=44285.459 E(kin)=11566.131 temperature=5731.504 | | Etotal =32719.327 grad(E)=221.036 E(BOND)=5365.524 E(ANGL)=8014.805 | | E(DIHE)=0.000 E(IMPR)=7024.153 E(VDW )=113.017 E(CDIH)=1609.399 | | E(NOE )=10305.635 E(PLAN)=286.795 | ------------------------------------------------------------------------------- NBONDS: found 13842 intra-atom interactions NBONDS: found 13820 intra-atom interactions NBONDS: found 13812 intra-atom interactions NBONDS: found 13785 intra-atom interactions NBONDS: found 13788 intra-atom interactions NBONDS: found 13753 intra-atom interactions NBONDS: found 13723 intra-atom interactions NBONDS: found 13706 intra-atom interactions NBONDS: found 13734 intra-atom interactions NBONDS: found 13757 intra-atom interactions NBONDS: found 13739 intra-atom interactions NBONDS: found 13750 intra-atom interactions NBONDS: found 13759 intra-atom interactions NBONDS: found 13760 intra-atom interactions NBONDS: found 13753 intra-atom interactions NBONDS: found 13769 intra-atom interactions NBONDS: found 13782 intra-atom interactions NBONDS: found 13801 intra-atom interactions NBONDS: found 13853 intra-atom interactions NBONDS: found 13896 intra-atom interactions NBONDS: found 13914 intra-atom interactions NBONDS: found 13923 intra-atom interactions NBONDS: found 13935 intra-atom interactions NBONDS: found 13916 intra-atom interactions NBONDS: found 13916 intra-atom interactions NBONDS: found 13928 intra-atom interactions NBONDS: found 13931 intra-atom interactions NBONDS: found 13953 intra-atom interactions NBONDS: found 13957 intra-atom interactions NBONDS: found 13963 intra-atom interactions NBONDS: found 13975 intra-atom interactions NBONDS: found 13993 intra-atom interactions NBONDS: found 13997 intra-atom interactions NBONDS: found 13996 intra-atom interactions NBONDS: found 13983 intra-atom interactions NBONDS: found 13969 intra-atom interactions --------------- step= 2000 at 4.00000 ps -------------------------------- | E(kin)+E(total)=46697.960 E(kin)=14337.629 temperature=7104.897 | | Etotal =32360.331 grad(E)=191.468 E(BOND)=5246.808 E(ANGL)=8341.894 | | E(DIHE)=0.000 E(IMPR)=3717.324 E(VDW )=116.709 E(CDIH)=1600.387 | | E(NOE )=12974.534 E(PLAN)=362.675 | ------------------------------------------------------------------------------- NBONDS: found 13951 intra-atom interactions NBONDS: found 13960 intra-atom interactions NBONDS: found 14003 intra-atom interactions NBONDS: found 14038 intra-atom interactions NBONDS: found 14060 intra-atom interactions NBONDS: found 14091 intra-atom interactions NBONDS: found 14107 intra-atom interactions NBONDS: found 14132 intra-atom interactions NBONDS: found 14150 intra-atom interactions NBONDS: found 14140 intra-atom interactions NBONDS: found 14105 intra-atom interactions NBONDS: found 14102 intra-atom interactions NBONDS: found 14082 intra-atom interactions NBONDS: found 14105 intra-atom interactions NBONDS: found 14116 intra-atom interactions NBONDS: found 14103 intra-atom interactions NBONDS: found 14077 intra-atom interactions NBONDS: found 14067 intra-atom interactions NBONDS: found 14067 intra-atom interactions NBONDS: found 14048 intra-atom interactions NBONDS: found 14034 intra-atom interactions NBONDS: found 14046 intra-atom interactions NBONDS: found 14039 intra-atom interactions NBONDS: found 14049 intra-atom interactions NBONDS: found 14057 intra-atom interactions NBONDS: found 14040 intra-atom interactions NBONDS: found 14027 intra-atom interactions NBONDS: found 14007 intra-atom interactions NBONDS: found 13994 intra-atom interactions NBONDS: found 13959 intra-atom interactions NBONDS: found 13917 intra-atom interactions NBONDS: found 13917 intra-atom interactions NBONDS: found 13905 intra-atom interactions NBONDS: found 13909 intra-atom interactions --------------- step= 2100 at 4.20000 ps -------------------------------- | E(kin)+E(total)=40530.239 E(kin)=9265.802 temperature=4591.594 | | Etotal =31264.437 grad(E)=271.710 E(BOND)=6079.403 E(ANGL)=9298.361 | | E(DIHE)=0.000 E(IMPR)=4172.965 E(VDW )=115.419 E(CDIH)=1553.807 | | E(NOE )=9766.105 E(PLAN)=278.378 | ------------------------------------------------------------------------------- NBONDS: found 13900 intra-atom interactions NBONDS: found 13858 intra-atom interactions NBONDS: found 13869 intra-atom interactions NBONDS: found 13868 intra-atom interactions NBONDS: found 13881 intra-atom interactions NBONDS: found 13897 intra-atom interactions NBONDS: found 13893 intra-atom interactions NBONDS: found 13902 intra-atom interactions NBONDS: found 13915 intra-atom interactions NBONDS: found 13920 intra-atom interactions NBONDS: found 13916 intra-atom interactions NBONDS: found 13918 intra-atom interactions NBONDS: found 13895 intra-atom interactions NBONDS: found 13899 intra-atom interactions NBONDS: found 13900 intra-atom interactions NBONDS: found 13885 intra-atom interactions NBONDS: found 13862 intra-atom interactions NBONDS: found 13866 intra-atom interactions NBONDS: found 13880 intra-atom interactions NBONDS: found 13883 intra-atom interactions NBONDS: found 13862 intra-atom interactions NBONDS: found 13852 intra-atom interactions NBONDS: found 13820 intra-atom interactions NBONDS: found 13799 intra-atom interactions NBONDS: found 13798 intra-atom interactions NBONDS: found 13763 intra-atom interactions NBONDS: found 13765 intra-atom interactions --------------- step= 2200 at 4.40000 ps -------------------------------- | E(kin)+E(total)=33083.383 E(kin)=7071.446 temperature=3504.199 | | Etotal =26011.936 grad(E)=176.889 E(BOND)=3520.999 E(ANGL)=7200.622 | | E(DIHE)=0.000 E(IMPR)=3071.013 E(VDW )=110.811 E(CDIH)=1688.151 | | E(NOE )=10116.413 E(PLAN)=303.927 | ------------------------------------------------------------------------------- NBONDS: found 13753 intra-atom interactions NBONDS: found 13719 intra-atom interactions NBONDS: found 13690 intra-atom interactions NBONDS: found 13710 intra-atom interactions NBONDS: found 13713 intra-atom interactions NBONDS: found 13732 intra-atom interactions NBONDS: found 13714 intra-atom interactions NBONDS: found 13671 intra-atom interactions NBONDS: found 13698 intra-atom interactions NBONDS: found 13702 intra-atom interactions NBONDS: found 13692 intra-atom interactions NBONDS: found 13670 intra-atom interactions NBONDS: found 13699 intra-atom interactions NBONDS: found 13718 intra-atom interactions NBONDS: found 13726 intra-atom interactions NBONDS: found 13736 intra-atom interactions NBONDS: found 13734 intra-atom interactions NBONDS: found 13750 intra-atom interactions NBONDS: found 13778 intra-atom interactions --------------- step= 2300 at 4.60000 ps -------------------------------- | E(kin)+E(total)=30981.684 E(kin)=6804.268 temperature=3371.801 | | Etotal =24177.416 grad(E)=134.231 E(BOND)=3146.525 E(ANGL)=7231.993 | | E(DIHE)=0.000 E(IMPR)=1876.422 E(VDW )=115.346 E(CDIH)=1640.709 | | E(NOE )=9846.902 E(PLAN)=319.519 | ------------------------------------------------------------------------------- NBONDS: found 13810 intra-atom interactions NBONDS: found 13822 intra-atom interactions NBONDS: found 13827 intra-atom interactions NBONDS: found 13820 intra-atom interactions NBONDS: found 13825 intra-atom interactions NBONDS: found 13819 intra-atom interactions NBONDS: found 13814 intra-atom interactions NBONDS: found 13852 intra-atom interactions NBONDS: found 13837 intra-atom interactions NBONDS: found 13848 intra-atom interactions NBONDS: found 13903 intra-atom interactions NBONDS: found 13924 intra-atom interactions NBONDS: found 13908 intra-atom interactions NBONDS: found 13910 intra-atom interactions NBONDS: found 13940 intra-atom interactions NBONDS: found 13965 intra-atom interactions NBONDS: found 13980 intra-atom interactions --------------- step= 2400 at 4.80000 ps -------------------------------- | E(kin)+E(total)=30813.978 E(kin)=6325.776 temperature=3134.688 | | Etotal =24488.202 grad(E)=164.982 E(BOND)=3623.844 E(ANGL)=7590.467 | | E(DIHE)=0.000 E(IMPR)=1815.551 E(VDW )=116.152 E(CDIH)=1480.413 | | E(NOE )=9567.872 E(PLAN)=293.902 | ------------------------------------------------------------------------------- NBONDS: found 13959 intra-atom interactions NBONDS: found 13965 intra-atom interactions NBONDS: found 13948 intra-atom interactions NBONDS: found 13916 intra-atom interactions NBONDS: found 13849 intra-atom interactions NBONDS: found 13884 intra-atom interactions NBONDS: found 13867 intra-atom interactions NBONDS: found 13848 intra-atom interactions NBONDS: found 13900 intra-atom interactions NBONDS: found 13892 intra-atom interactions NBONDS: found 13864 intra-atom interactions NBONDS: found 13859 intra-atom interactions NBONDS: found 13841 intra-atom interactions NBONDS: found 13817 intra-atom interactions --------------- step= 2500 at 5.00000 ps -------------------------------- | E(kin)+E(total)=31323.204 E(kin)=6215.642 temperature=3080.111 | | Etotal =25107.562 grad(E)=166.961 E(BOND)=3232.562 E(ANGL)=7305.224 | | E(DIHE)=0.000 E(IMPR)=2463.827 E(VDW )=112.383 E(CDIH)=1650.761 | | E(NOE )=9998.193 E(PLAN)=344.611 | ------------------------------------------------------------------------------- NBONDS: found 13850 intra-atom interactions NBONDS: found 13903 intra-atom interactions NBONDS: found 13899 intra-atom interactions %atoms "A -2 -GUA -N2 " and "A -3 -CYT -C5' " only 0.01 A apart NBONDS: found 13927 intra-atom interactions NBONDS: found 13917 intra-atom interactions NBONDS: found 13918 intra-atom interactions NBONDS: found 13953 intra-atom interactions NBONDS: found 13878 intra-atom interactions NBONDS: found 13835 intra-atom interactions NBONDS: found 13833 intra-atom interactions NBONDS: found 13830 intra-atom interactions NBONDS: found 13837 intra-atom interactions NBONDS: found 13833 intra-atom interactions NBONDS: found 13896 intra-atom interactions --------------- step= 2600 at 5.20000 ps -------------------------------- | E(kin)+E(total)=32010.605 E(kin)=6357.994 temperature=3150.653 | | Etotal =25652.611 grad(E)=170.822 E(BOND)=3987.335 E(ANGL)=7583.427 | | E(DIHE)=0.000 E(IMPR)=2289.059 E(VDW )=115.459 E(CDIH)=1609.850 | | E(NOE )=9703.457 E(PLAN)=364.025 | ------------------------------------------------------------------------------- NBONDS: found 13942 intra-atom interactions NBONDS: found 13936 intra-atom interactions NBONDS: found 13955 intra-atom interactions NBONDS: found 13978 intra-atom interactions NBONDS: found 13934 intra-atom interactions NBONDS: found 13939 intra-atom interactions NBONDS: found 13937 intra-atom interactions NBONDS: found 13951 intra-atom interactions NBONDS: found 13960 intra-atom interactions NBONDS: found 13920 intra-atom interactions NBONDS: found 13905 intra-atom interactions NBONDS: found 13915 intra-atom interactions NBONDS: found 13921 intra-atom interactions --------------- step= 2700 at 5.40000 ps -------------------------------- | E(kin)+E(total)=30702.706 E(kin)=6032.225 temperature=2989.221 | | Etotal =24670.481 grad(E)=150.146 E(BOND)=3584.062 E(ANGL)=7250.574 | | E(DIHE)=0.000 E(IMPR)=1763.495 E(VDW )=113.657 E(CDIH)=1716.470 | | E(NOE )=9932.760 E(PLAN)=309.463 | ------------------------------------------------------------------------------- NBONDS: found 13942 intra-atom interactions NBONDS: found 13918 intra-atom interactions NBONDS: found 13913 intra-atom interactions NBONDS: found 13922 intra-atom interactions NBONDS: found 13905 intra-atom interactions NBONDS: found 13895 intra-atom interactions NBONDS: found 13904 intra-atom interactions NBONDS: found 13925 intra-atom interactions NBONDS: found 13940 intra-atom interactions NBONDS: found 13977 intra-atom interactions NBONDS: found 13992 intra-atom interactions --------------- step= 2800 at 5.60000 ps -------------------------------- | E(kin)+E(total)=31088.424 E(kin)=6801.910 temperature=3370.632 | | Etotal =24286.514 grad(E)=141.964 E(BOND)=3114.210 E(ANGL)=7455.230 | | E(DIHE)=0.000 E(IMPR)=1890.158 E(VDW )=115.874 E(CDIH)=1841.060 | | E(NOE )=9560.104 E(PLAN)=309.877 | ------------------------------------------------------------------------------- NBONDS: found 13983 intra-atom interactions NBONDS: found 13946 intra-atom interactions NBONDS: found 13958 intra-atom interactions NBONDS: found 13995 intra-atom interactions NBONDS: found 13967 intra-atom interactions NBONDS: found 14006 intra-atom interactions NBONDS: found 13998 intra-atom interactions NBONDS: found 13990 intra-atom interactions NBONDS: found 14005 intra-atom interactions NBONDS: found 13958 intra-atom interactions NBONDS: found 13922 intra-atom interactions NBONDS: found 13913 intra-atom interactions NBONDS: found 13921 intra-atom interactions NBONDS: found 13967 intra-atom interactions NBONDS: found 13907 intra-atom interactions NBONDS: found 13902 intra-atom interactions --------------- step= 2900 at 5.80000 ps -------------------------------- | E(kin)+E(total)=31575.061 E(kin)=6477.342 temperature=3209.795 | | Etotal =25097.719 grad(E)=173.057 E(BOND)=3742.454 E(ANGL)=7550.766 | | E(DIHE)=0.000 E(IMPR)=2104.743 E(VDW )=114.940 E(CDIH)=1752.998 | | E(NOE )=9512.266 E(PLAN)=319.552 | ------------------------------------------------------------------------------- NBONDS: found 13866 intra-atom interactions NBONDS: found 13862 intra-atom interactions NBONDS: found 13809 intra-atom interactions NBONDS: found 13721 intra-atom interactions NBONDS: found 13686 intra-atom interactions NBONDS: found 13669 intra-atom interactions NBONDS: found 13684 intra-atom interactions NBONDS: found 13625 intra-atom interactions NBONDS: found 13612 intra-atom interactions NBONDS: found 13611 intra-atom interactions NBONDS: found 13598 intra-atom interactions NBONDS: found 13576 intra-atom interactions NBONDS: found 13552 intra-atom interactions --------------- step= 3000 at 6.00000 ps -------------------------------- | E(kin)+E(total)=31410.311 E(kin)=5896.058 temperature=2921.744 | | Etotal =25514.253 grad(E)=163.926 E(BOND)=3633.879 E(ANGL)=7595.656 | | E(DIHE)=0.000 E(IMPR)=2099.986 E(VDW )=107.455 E(CDIH)=1787.770 | | E(NOE )=9984.984 E(PLAN)=304.523 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : -0.00001 0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> constraints inter (all) (all) weights * 1 dihe 1 impr 1 vdw 0.003 end end SELRPN: 677 atoms have been selected out of 677 SELRPN: 677 atoms have been selected out of 677 X-PLOR> dynamics verlet DYNAmics> nstep=$nstep1 time=$high_timestep iasvel=current firstt=$init_t DYNAmics> tcoup=true tbath=$init_t nprint=100 iprfrq=0 DYNAmics> end DYNAMC: number of degrees of freedom= 2031 ASSVEL: current velocities taken. CENMAS: Information about center of free masses position [A] : -0.00001 0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : -0.00001 0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 NBONDS: generating intra-molecular exclusion list with mode=-3 MAKINB: mode -3 found 2027 exclusions and 0 interactions(1-4) NBONDS: found 13552 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=51404.593 E(kin)=5896.058 temperature=2921.744 | | Etotal =45508.535 grad(E)=404.763 E(BOND)=9084.698 E(ANGL)=18989.139 | | E(DIHE)=0.000 E(IMPR)=5249.966 E(VDW )=107.455 E(CDIH)=1787.770 | | E(NOE )=9984.984 E(PLAN)=304.523 | ------------------------------------------------------------------------------- NBONDS: found 13566 intra-atom interactions NBONDS: found 13604 intra-atom interactions NBONDS: found 13653 intra-atom interactions NBONDS: found 13648 intra-atom interactions NBONDS: found 13679 intra-atom interactions NBONDS: found 13686 intra-atom interactions NBONDS: found 13736 intra-atom interactions NBONDS: found 13772 intra-atom interactions NBONDS: found 13799 intra-atom interactions NBONDS: found 13824 intra-atom interactions NBONDS: found 13860 intra-atom interactions NBONDS: found 13943 intra-atom interactions NBONDS: found 13946 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=41004.234 E(kin)=7310.398 temperature=3622.609 | | Etotal =33693.836 grad(E)=252.941 E(BOND)=3419.498 E(ANGL)=12140.446 | | E(DIHE)=0.000 E(IMPR)=2025.297 E(VDW )=113.446 E(CDIH)=1852.518 | | E(NOE )=13706.004 E(PLAN)=436.628 | ------------------------------------------------------------------------------- NBONDS: found 13893 intra-atom interactions NBONDS: found 13939 intra-atom interactions NBONDS: found 13950 intra-atom interactions NBONDS: found 13995 intra-atom interactions NBONDS: found 14073 intra-atom interactions NBONDS: found 14139 intra-atom interactions NBONDS: found 14148 intra-atom interactions NBONDS: found 14127 intra-atom interactions NBONDS: found 14203 intra-atom interactions NBONDS: found 14169 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=39312.869 E(kin)=6360.061 temperature=3151.677 | | Etotal =32952.808 grad(E)=230.476 E(BOND)=3275.297 E(ANGL)=10661.253 | | E(DIHE)=0.000 E(IMPR)=2229.838 E(VDW )=118.816 E(CDIH)=1771.559 | | E(NOE )=14505.434 E(PLAN)=390.611 | ------------------------------------------------------------------------------- NBONDS: found 14206 intra-atom interactions NBONDS: found 14258 intra-atom interactions NBONDS: found 14309 intra-atom interactions NBONDS: found 14277 intra-atom interactions NBONDS: found 14306 intra-atom interactions NBONDS: found 14321 intra-atom interactions NBONDS: found 14368 intra-atom interactions NBONDS: found 14361 intra-atom interactions NBONDS: found 14331 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=38991.248 E(kin)=6514.766 temperature=3228.340 | | Etotal =32476.482 grad(E)=219.056 E(BOND)=3091.759 E(ANGL)=10182.970 | | E(DIHE)=0.000 E(IMPR)=1908.299 E(VDW )=119.572 E(CDIH)=1818.993 | | E(NOE )=14932.488 E(PLAN)=422.400 | ------------------------------------------------------------------------------- NBONDS: found 14328 intra-atom interactions NBONDS: found 14346 intra-atom interactions NBONDS: found 14350 intra-atom interactions NBONDS: found 14351 intra-atom interactions NBONDS: found 14341 intra-atom interactions NBONDS: found 14369 intra-atom interactions NBONDS: found 14378 intra-atom interactions NBONDS: found 14439 intra-atom interactions NBONDS: found 14484 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=38792.422 E(kin)=6104.866 temperature=3025.218 | | Etotal =32687.556 grad(E)=221.247 E(BOND)=2941.172 E(ANGL)=10857.993 | | E(DIHE)=0.000 E(IMPR)=1923.486 E(VDW )=122.496 E(CDIH)=1859.995 | | E(NOE )=14566.501 E(PLAN)=415.913 | ------------------------------------------------------------------------------- NBONDS: found 14497 intra-atom interactions NBONDS: found 14515 intra-atom interactions NBONDS: found 14558 intra-atom interactions NBONDS: found 14623 intra-atom interactions NBONDS: found 14612 intra-atom interactions NBONDS: found 14698 intra-atom interactions NBONDS: found 14723 intra-atom interactions NBONDS: found 14744 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=38798.496 E(kin)=6176.120 temperature=3060.527 | | Etotal =32622.376 grad(E)=209.461 E(BOND)=3282.620 E(ANGL)=10669.707 | | E(DIHE)=0.000 E(IMPR)=1987.481 E(VDW )=127.838 E(CDIH)=1675.587 | | E(NOE )=14418.620 E(PLAN)=460.524 | ------------------------------------------------------------------------------- NBONDS: found 14752 intra-atom interactions NBONDS: found 14772 intra-atom interactions NBONDS: found 14901 intra-atom interactions NBONDS: found 14890 intra-atom interactions NBONDS: found 14907 intra-atom interactions NBONDS: found 14961 intra-atom interactions NBONDS: found 15048 intra-atom interactions NBONDS: found 15098 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=38790.591 E(kin)=6115.366 temperature=3030.421 | | Etotal =32675.225 grad(E)=214.350 E(BOND)=3263.315 E(ANGL)=10207.611 | | E(DIHE)=0.000 E(IMPR)=1910.016 E(VDW )=132.402 E(CDIH)=1815.891 | | E(NOE )=14877.508 E(PLAN)=468.482 | ------------------------------------------------------------------------------- NBONDS: found 15175 intra-atom interactions NBONDS: found 15227 intra-atom interactions NBONDS: found 15350 intra-atom interactions NBONDS: found 15420 intra-atom interactions NBONDS: found 15434 intra-atom interactions NBONDS: found 15431 intra-atom interactions NBONDS: found 15515 intra-atom interactions NBONDS: found 15572 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=38696.815 E(kin)=6427.664 temperature=3185.177 | | Etotal =32269.152 grad(E)=204.726 E(BOND)=3133.805 E(ANGL)=9743.054 | | E(DIHE)=0.000 E(IMPR)=1870.507 E(VDW )=138.000 E(CDIH)=2028.558 | | E(NOE )=14883.510 E(PLAN)=471.718 | ------------------------------------------------------------------------------- NBONDS: found 15672 intra-atom interactions NBONDS: found 15726 intra-atom interactions NBONDS: found 15806 intra-atom interactions CENMAS: Information about center of free masses position [A] : -0.00001 0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> if ($image=1) then NEXTCD: condition evaluated as true X-PLOR> vector do (store7=x) (all) ! Store first image in stores. SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store8=y) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store9=z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store4=vx) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store5=vy) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store6=vz) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> end if X-PLOR> X-PLOR>end loop imag X-PLOR>for $image in (1 -1) loop imag FOR LOOP: symbol IMAGE set to -1.00000 (real) X-PLOR> X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates COOR>REMARK FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/dg.pdb" COOR>REMARK DATE:16-Aug-96 18:13:27 created by user: COOR>ATOM 1 P GUA 1 10.530 3.172 10.479 1.00 0.00 A COOR>ATOM 2 O1P GUA 1 13.528 5.873 7.438 1.00 0.00 A X-PLOR> X-PLOR> ! END in PDB file X-PLOR> vector do (x=x * $image) (known) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector identity (store1) (not known) ! Set store1 to unknowns. SELRPN: 0 atoms have been selected out of 677 X-PLOR> X-PLOR> ! Create local ideal geometry by template fitting; X-PLOR> ! this also takes care of unknown atoms. X-PLOR> X-PLOR> coordinates copy end ! Store current coordinates in comparison set. COOR: selected main coordinates copied to comp X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates COOR>REMARK 5 FILENAME="/sgi/people/dcs/ws/xplor/italy2.4x/template.pdb" COOR>REMARK 5 DATE:27-Apr-96 13:42:54 created by user: COOR>ATOM 1 P GUA A 1 -7.862 1.642 2.093 1.00 0.00 A COOR>ATOM 2 O1P GUA A 1 -9.267 1.385 1.685 1.00 0.00 A X-PLOR> X-PLOR> ! END in PDB file X-PLOR> X-PLOR> set echo=off message=off end R.m.s. diff. between fitted set and comp. set for selected atoms = 3.0318 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.7627 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0110 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9472 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0058 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9247 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1225 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.1666 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.4396 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6257 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.8476 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.6908 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.3475 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.4624 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1644 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1248 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.5916 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8619 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.3993 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8943 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.5551 X-PLOR> X-PLOR> coordinates swap end COOR: selected coordinates swaped (main<->comp) X-PLOR> X-PLOR> ! Minimization of bonds, VDWs, and NOEs. X-PLOR> X-PLOR> flags exclude * include bond vdw noe cdih plan end X-PLOR> constraints interaction (all) (all) weights * 1 vdw 20 end end SELRPN: 677 atoms have been selected out of 677 SELRPN: 677 atoms have been selected out of 677 X-PLOR> parameter nbonds nbxmod=-2 repel=0.5 end end X-PLOR> restraints dihedral scale=20 end X-PLOR> minimize powell drop=10 nstep=300 nprint=10 end POWELL: number of degrees of freedom= 2031 CODBON: bond type-based parameters retrieved NBUPDA: type-based van der Waals parameters retrieved. NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 728 exclusions and 0 interactions(1-4) NBONDS: found 15768 intra-atom interactions NBONDS: found 15808 intra-atom interactions NBONDS: found 15882 intra-atom interactions NBONDS: found 15962 intra-atom interactions NBONDS: found 16064 intra-atom interactions NBONDS: found 16112 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0002 ----------------------- | Etotal =103601.766 grad(E)=298.217 E(BOND)=12991.467 E(VDW )=12154.366 | | E(CDIH)=4145.311 E(NOE )=73776.392 E(PLAN)=534.230 | ------------------------------------------------------------------------------- NBONDS: found 16114 intra-atom interactions NBONDS: found 16147 intra-atom interactions NBONDS: found 16170 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =59154.687 grad(E)=154.555 E(BOND)=4004.771 E(VDW )=7986.557 | | E(CDIH)=3105.923 E(NOE )=43651.522 E(PLAN)=405.913 | ------------------------------------------------------------------------------- NBONDS: found 16120 intra-atom interactions NBONDS: found 15949 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0002 ----------------------- | Etotal =42257.260 grad(E)=125.646 E(BOND)=2267.286 E(VDW )=6076.953 | | E(CDIH)=2344.434 E(NOE )=31274.792 E(PLAN)=293.796 | ------------------------------------------------------------------------------- NBONDS: found 15780 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =33017.650 grad(E)=84.711 E(BOND)=1432.266 E(VDW )=4265.105 | | E(CDIH)=1819.824 E(NOE )=25174.192 E(PLAN)=326.262 | ------------------------------------------------------------------------------- NBONDS: found 15699 intra-atom interactions NBONDS: found 15560 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =27005.283 grad(E)=79.086 E(BOND)=1036.780 E(VDW )=3376.049 | | E(CDIH)=1845.516 E(NOE )=20454.140 E(PLAN)=292.798 | ------------------------------------------------------------------------------- NBONDS: found 15447 intra-atom interactions NBONDS: found 15362 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =23572.307 grad(E)=65.094 E(BOND)=672.911 E(VDW )=2885.617 | | E(CDIH)=1805.923 E(NOE )=17955.158 E(PLAN)=252.699 | ------------------------------------------------------------------------------- NBONDS: found 15346 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =20340.932 grad(E)=58.476 E(BOND)=582.068 E(VDW )=2229.748 | | E(CDIH)=1570.753 E(NOE )=15710.225 E(PLAN)=248.138 | ------------------------------------------------------------------------------- NBONDS: found 15253 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =18295.669 grad(E)=47.980 E(BOND)=502.923 E(VDW )=1894.045 | | E(CDIH)=1578.687 E(NOE )=14077.278 E(PLAN)=242.736 | ------------------------------------------------------------------------------- NBONDS: found 15184 intra-atom interactions NBONDS: found 15119 intra-atom interactions NBONDS: found 15175 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =16617.815 grad(E)=35.839 E(BOND)=352.567 E(VDW )=1673.147 | | E(CDIH)=1403.437 E(NOE )=12953.420 E(PLAN)=235.243 | ------------------------------------------------------------------------------- NBONDS: found 15136 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =15273.983 grad(E)=28.556 E(BOND)=320.229 E(VDW )=1515.964 | | E(CDIH)=1165.776 E(NOE )=12045.645 E(PLAN)=226.370 | ------------------------------------------------------------------------------- --------------- cycle= 110 ------ stepsize= 0.0001 ----------------------- | Etotal =14449.980 grad(E)=36.826 E(BOND)=362.326 E(VDW )=1349.944 | | E(CDIH)=1235.509 E(NOE )=11270.928 E(PLAN)=231.274 | ------------------------------------------------------------------------------- NBONDS: found 14985 intra-atom interactions NBONDS: found 15110 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0000 ----------------------- | Etotal =13718.300 grad(E)=27.380 E(BOND)=303.984 E(VDW )=1302.207 | | E(CDIH)=1121.510 E(NOE )=10757.567 E(PLAN)=233.032 | ------------------------------------------------------------------------------- --------------- cycle= 130 ------ stepsize= 0.0000 ----------------------- | Etotal =13609.340 grad(E)=26.157 E(BOND)=292.140 E(VDW )=1285.064 | | E(CDIH)=1111.596 E(NOE )=10686.259 E(PLAN)=234.281 | ------------------------------------------------------------------------------- --------------- cycle= 140 ------ stepsize= 0.0000 ----------------------- | Etotal =13609.123 grad(E)=26.180 E(BOND)=292.198 E(VDW )=1285.018 | | E(CDIH)=1111.568 E(NOE )=10686.053 E(PLAN)=234.284 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =13609.082 grad(E)=26.184 E(BOND)=292.209 E(VDW )=1285.010 | | E(CDIH)=1111.563 E(NOE )=10686.015 E(PLAN)=234.285 | ------------------------------------------------------------------------------- --------------- cycle= 160 ------ stepsize= 0.0000 ----------------------- | Etotal =13844.585 grad(E)=56.204 E(BOND)=292.211 E(VDW )=1285.008 | | E(CDIH)=1347.075 E(NOE )=10686.005 E(PLAN)=234.285 | ------------------------------------------------------------------------------- --------------- cycle= 170 ------ stepsize= 0.0000 ----------------------- | Etotal =13609.072 grad(E)=26.185 E(BOND)=292.211 E(VDW )=1285.008 | | E(CDIH)=1111.562 E(NOE )=10686.006 E(PLAN)=234.285 | ------------------------------------------------------------------------------- --------------- cycle= 180 ------ stepsize= 0.0000 ----------------------- | Etotal =13844.586 grad(E)=56.204 E(BOND)=292.211 E(VDW )=1285.008 | | E(CDIH)=1347.075 E(NOE )=10686.006 E(PLAN)=234.285 | ------------------------------------------------------------------------------- %POWELL-ERR: Line search abandoned POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR> ! Include angles. X-PLOR> X-PLOR> flags include angl end X-PLOR> minimize powell drop=10 nstep=300 nprint=10 end POWELL: number of degrees of freedom= 2031 CODANG: angle type-based parameters retrieved NBONDS: found 15067 intra-atom interactions NBONDS: found 15008 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =98257.357 grad(E)=338.112 E(BOND)=13118.713 E(ANGL)=62609.079 | | E(VDW )=3491.411 E(CDIH)=2750.892 E(NOE )=15825.453 E(PLAN)=461.809 | ------------------------------------------------------------------------------- NBONDS: found 14910 intra-atom interactions NBONDS: found 14933 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =67182.253 grad(E)=167.785 E(BOND)=4871.304 E(ANGL)=34554.724 | | E(VDW )=3976.082 E(CDIH)=3346.310 E(NOE )=19998.986 E(PLAN)=434.846 | ------------------------------------------------------------------------------- NBONDS: found 14886 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =58311.322 grad(E)=103.717 E(BOND)=2890.535 E(ANGL)=25372.348 | | E(VDW )=4324.636 E(CDIH)=3541.279 E(NOE )=21756.104 E(PLAN)=426.420 | ------------------------------------------------------------------------------- NBONDS: found 14783 intra-atom interactions NBONDS: found 14667 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =53042.151 grad(E)=107.751 E(BOND)=2747.976 E(ANGL)=22104.902 | | E(VDW )=3869.912 E(CDIH)=3424.817 E(NOE )=20500.669 E(PLAN)=393.876 | ------------------------------------------------------------------------------- NBONDS: found 14508 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =48817.245 grad(E)=78.703 E(BOND)=2142.056 E(ANGL)=19260.123 | | E(VDW )=3446.513 E(CDIH)=3214.172 E(NOE )=20371.954 E(PLAN)=382.426 | ------------------------------------------------------------------------------- NBONDS: found 14373 intra-atom interactions NBONDS: found 14225 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =44777.881 grad(E)=85.978 E(BOND)=2257.685 E(ANGL)=16665.837 | | E(VDW )=2933.758 E(CDIH)=3140.191 E(NOE )=19409.614 E(PLAN)=370.796 | ------------------------------------------------------------------------------- NBONDS: found 14143 intra-atom interactions NBONDS: found 14022 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =40922.552 grad(E)=87.234 E(BOND)=2058.943 E(ANGL)=14078.048 | | E(VDW )=2661.112 E(CDIH)=3261.170 E(NOE )=18480.239 E(PLAN)=383.040 | ------------------------------------------------------------------------------- NBONDS: found 13991 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =38228.628 grad(E)=58.795 E(BOND)=1682.509 E(ANGL)=12650.256 | | E(VDW )=2569.564 E(CDIH)=3234.322 E(NOE )=17716.739 E(PLAN)=375.237 | ------------------------------------------------------------------------------- NBONDS: found 13868 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =36240.675 grad(E)=59.641 E(BOND)=1581.931 E(ANGL)=11912.516 | | E(VDW )=2418.013 E(CDIH)=3217.594 E(NOE )=16745.938 E(PLAN)=364.682 | ------------------------------------------------------------------------------- NBONDS: found 13799 intra-atom interactions NBONDS: found 13656 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =34677.349 grad(E)=46.416 E(BOND)=1527.873 E(ANGL)=11365.791 | | E(VDW )=2244.020 E(CDIH)=3205.081 E(NOE )=16000.705 E(PLAN)=333.879 | ------------------------------------------------------------------------------- NBONDS: found 13528 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0001 ----------------------- | Etotal =33360.485 grad(E)=45.809 E(BOND)=1579.016 E(ANGL)=10918.230 | | E(VDW )=2040.648 E(CDIH)=3228.064 E(NOE )=15299.565 E(PLAN)=294.962 | ------------------------------------------------------------------------------- NBONDS: found 13420 intra-atom interactions NBONDS: found 13317 intra-atom interactions NBONDS: found 13222 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0001 ----------------------- | Etotal =31165.491 grad(E)=62.721 E(BOND)=1608.396 E(ANGL)=9699.304 | | E(VDW )=1778.536 E(CDIH)=3273.034 E(NOE )=14527.494 E(PLAN)=278.727 | ------------------------------------------------------------------------------- NBONDS: found 13104 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0001 ----------------------- | Etotal =29283.888 grad(E)=52.893 E(BOND)=1366.501 E(ANGL)=8367.021 | | E(VDW )=1724.838 E(CDIH)=3219.782 E(NOE )=14316.274 E(PLAN)=289.472 | ------------------------------------------------------------------------------- NBONDS: found 13002 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0001 ----------------------- | Etotal =27795.864 grad(E)=46.099 E(BOND)=1144.827 E(ANGL)=7718.777 | | E(VDW )=1775.748 E(CDIH)=3105.755 E(NOE )=13752.681 E(PLAN)=298.077 | ------------------------------------------------------------------------------- NBONDS: found 12931 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =26765.612 grad(E)=42.109 E(BOND)=1033.120 E(ANGL)=7287.759 | | E(VDW )=1837.747 E(CDIH)=3032.257 E(NOE )=13283.882 E(PLAN)=290.846 | ------------------------------------------------------------------------------- NBONDS: found 12852 intra-atom interactions --------------- cycle= 160 ------ stepsize= 0.0001 ----------------------- | Etotal =25921.711 grad(E)=38.583 E(BOND)=1004.871 E(ANGL)=7158.046 | | E(VDW )=1844.120 E(CDIH)=2876.202 E(NOE )=12759.738 E(PLAN)=278.735 | ------------------------------------------------------------------------------- --------------- cycle= 170 ------ stepsize= 0.0001 ----------------------- | Etotal =25157.683 grad(E)=36.715 E(BOND)=987.459 E(ANGL)=7040.881 | | E(VDW )=1674.768 E(CDIH)=2737.827 E(NOE )=12445.781 E(PLAN)=270.967 | ------------------------------------------------------------------------------- NBONDS: found 12799 intra-atom interactions --------------- cycle= 180 ------ stepsize= 0.0001 ----------------------- | Etotal =24511.515 grad(E)=34.208 E(BOND)=965.848 E(ANGL)=6851.342 | | E(VDW )=1517.578 E(CDIH)=2647.144 E(NOE )=12265.971 E(PLAN)=263.632 | ------------------------------------------------------------------------------- NBONDS: found 12720 intra-atom interactions NBONDS: found 12658 intra-atom interactions --------------- cycle= 190 ------ stepsize= 0.0001 ----------------------- | Etotal =23584.179 grad(E)=49.015 E(BOND)=980.335 E(ANGL)=6072.547 | | E(VDW )=1376.005 E(CDIH)=2566.436 E(NOE )=12337.179 E(PLAN)=251.677 | ------------------------------------------------------------------------------- NBONDS: found 12644 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =22777.341 grad(E)=43.067 E(BOND)=890.464 E(ANGL)=5848.725 | | E(VDW )=1287.312 E(CDIH)=2475.743 E(NOE )=12024.968 E(PLAN)=250.130 | ------------------------------------------------------------------------------- NBONDS: found 12614 intra-atom interactions --------------- cycle= 210 ------ stepsize= 0.0001 ----------------------- | Etotal =22186.191 grad(E)=25.712 E(BOND)=821.981 E(ANGL)=5530.825 | | E(VDW )=1263.427 E(CDIH)=2422.291 E(NOE )=11900.704 E(PLAN)=246.964 | ------------------------------------------------------------------------------- NBONDS: found 12581 intra-atom interactions --------------- cycle= 220 ------ stepsize= 0.0001 ----------------------- | Etotal =21779.636 grad(E)=26.079 E(BOND)=778.768 E(ANGL)=5464.778 | | E(VDW )=1194.406 E(CDIH)=2387.151 E(NOE )=11717.132 E(PLAN)=237.402 | ------------------------------------------------------------------------------- --------------- cycle= 230 ------ stepsize= 0.0001 ----------------------- | Etotal =21427.353 grad(E)=25.837 E(BOND)=788.300 E(ANGL)=5453.942 | | E(VDW )=1115.846 E(CDIH)=2364.743 E(NOE )=11471.547 E(PLAN)=232.975 | ------------------------------------------------------------------------------- NBONDS: found 12498 intra-atom interactions --------------- cycle= 240 ------ stepsize= 0.0001 --------------------