X-PLOR: V3.840 user: on: Alpha/OSF at: 16-Aug-96 18:25:49 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=100060.514923096 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 18:25:48 created by user: COOR>ATOM 1 P GUA 1 12.148 5.107 8.580 1.00 0.00 A COOR>ATOM 2 O1P GUA 1 12.456 4.522 8.142 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 = 2.8197 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6852 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1560 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.3497 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.3035 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2036 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.5109 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.2900 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.1660 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.1438 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.7733 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.9178 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.1112 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.2289 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.5153 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1735 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 = 2.1122 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.8910 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0885 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.8942 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 14766 intra-atom interactions NBONDS: found 14840 intra-atom interactions NBONDS: found 14976 intra-atom interactions NBONDS: found 15116 intra-atom interactions NBONDS: found 15357 intra-atom interactions NBONDS: found 15597 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0002 ----------------------- | Etotal =111026.404 grad(E)=329.258 E(BOND)=13630.880 E(VDW )=9248.587 | | E(CDIH)=4317.611 E(NOE )=83193.338 E(PLAN)=635.988 | ------------------------------------------------------------------------------- NBONDS: found 15702 intra-atom interactions NBONDS: found 15860 intra-atom interactions NBONDS: found 15884 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0002 ----------------------- | Etotal =65469.250 grad(E)=188.444 E(BOND)=5250.361 E(VDW )=7501.850 | | E(CDIH)=3183.657 E(NOE )=49066.603 E(PLAN)=466.779 | ------------------------------------------------------------------------------- NBONDS: found 15916 intra-atom interactions NBONDS: found 15928 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =48288.370 grad(E)=103.653 E(BOND)=2012.621 E(VDW )=5751.652 | | E(CDIH)=2900.380 E(NOE )=37273.180 E(PLAN)=350.538 | ------------------------------------------------------------------------------- NBONDS: found 15912 intra-atom interactions NBONDS: found 15899 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0002 ----------------------- | Etotal =38790.126 grad(E)=86.559 E(BOND)=1688.376 E(VDW )=4491.954 | | E(CDIH)=2636.953 E(NOE )=29625.425 E(PLAN)=347.419 | ------------------------------------------------------------------------------- NBONDS: found 15870 intra-atom interactions NBONDS: found 15857 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0002 ----------------------- | Etotal =32117.729 grad(E)=83.438 E(BOND)=1224.089 E(VDW )=3276.871 | | E(CDIH)=2937.657 E(NOE )=24321.420 E(PLAN)=357.691 | ------------------------------------------------------------------------------- NBONDS: found 15818 intra-atom interactions --------------- cycle= 60 ------ stepsize= -0.0001 ----------------------- | Etotal =28176.346 grad(E)=69.623 E(BOND)=1192.910 E(VDW )=2904.918 | | E(CDIH)=2665.311 E(NOE )=21058.463 E(PLAN)=354.744 | ------------------------------------------------------------------------------- NBONDS: found 15765 intra-atom interactions NBONDS: found 15721 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =24734.495 grad(E)=50.583 E(BOND)=870.666 E(VDW )=2308.321 | | E(CDIH)=2572.923 E(NOE )=18664.461 E(PLAN)=318.124 | ------------------------------------------------------------------------------- NBONDS: found 15679 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0002 ----------------------- | Etotal =21859.963 grad(E)=51.119 E(BOND)=633.003 E(VDW )=1828.417 | | E(CDIH)=2340.686 E(NOE )=16740.951 E(PLAN)=316.906 | ------------------------------------------------------------------------------- NBONDS: found 15569 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =19976.782 grad(E)=43.610 E(BOND)=597.204 E(VDW )=1511.439 | | E(CDIH)=2130.800 E(NOE )=15410.707 E(PLAN)=326.633 | ------------------------------------------------------------------------------- NBONDS: found 15531 intra-atom interactions NBONDS: found 15446 intra-atom interactions NBONDS: found 15530 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =18640.346 grad(E)=41.472 E(BOND)=465.024 E(VDW )=1381.020 | | E(CDIH)=1692.079 E(NOE )=14782.450 E(PLAN)=319.773 | ------------------------------------------------------------------------------- NBONDS: found 15477 intra-atom interactions NBONDS: found 15418 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0001 ----------------------- | Etotal =16904.492 grad(E)=30.062 E(BOND)=362.979 E(VDW )=1300.761 | | E(CDIH)=1051.480 E(NOE )=13917.162 E(PLAN)=272.109 | ------------------------------------------------------------------------------- NBONDS: found 15389 intra-atom interactions NBONDS: found 15162 intra-atom interactions NBONDS: found 15384 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0000 ----------------------- | Etotal =16346.050 grad(E)=59.694 E(BOND)=450.536 E(VDW )=1218.457 | | E(CDIH)=1276.889 E(NOE )=13160.125 E(PLAN)=240.043 | ------------------------------------------------------------------------------- --------------- cycle= 130 ------ stepsize= 0.0000 ----------------------- | Etotal =16124.432 grad(E)=36.209 E(BOND)=426.143 E(VDW )=1212.455 | | E(CDIH)=1021.252 E(NOE )=13221.990 E(PLAN)=242.591 | ------------------------------------------------------------------------------- --------------- cycle= 140 ------ stepsize= 0.0000 ----------------------- | Etotal =16399.943 grad(E)=63.488 E(BOND)=426.150 E(VDW )=1212.459 | | E(CDIH)=1296.808 E(NOE )=13221.937 E(PLAN)=242.589 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =16124.405 grad(E)=36.209 E(BOND)=426.146 E(VDW )=1212.457 | | E(CDIH)=1021.246 E(NOE )=13221.966 E(PLAN)=242.590 | ------------------------------------------------------------------------------- --------------- cycle= 160 ------ stepsize= 0.0000 ----------------------- | Etotal =16124.405 grad(E)=36.209 E(BOND)=426.146 E(VDW )=1212.457 | | E(CDIH)=1021.246 E(NOE )=13221.966 E(PLAN)=242.590 | ------------------------------------------------------------------------------- %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 15388 intra-atom interactions NBONDS: found 15384 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =96226.351 grad(E)=315.255 E(BOND)=13105.926 E(ANGL)=58753.032 | | E(VDW )=3494.492 E(CDIH)=2953.698 E(NOE )=17265.699 E(PLAN)=653.504 | ------------------------------------------------------------------------------- NBONDS: found 15372 intra-atom interactions NBONDS: found 15340 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =65742.384 grad(E)=168.063 E(BOND)=4055.647 E(ANGL)=31222.616 | | E(VDW )=3987.807 E(CDIH)=3478.634 E(NOE )=22268.447 E(PLAN)=729.232 | ------------------------------------------------------------------------------- NBONDS: found 15354 intra-atom interactions NBONDS: found 15259 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =55409.668 grad(E)=106.781 E(BOND)=2923.276 E(ANGL)=22293.942 | | E(VDW )=3517.138 E(CDIH)=3604.868 E(NOE )=22357.709 E(PLAN)=712.735 | ------------------------------------------------------------------------------- NBONDS: found 15208 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =49869.519 grad(E)=113.279 E(BOND)=2443.980 E(ANGL)=17380.594 | | E(VDW )=3145.072 E(CDIH)=3688.212 E(NOE )=22543.689 E(PLAN)=667.973 | ------------------------------------------------------------------------------- NBONDS: found 15124 intra-atom interactions NBONDS: found 15043 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =46629.202 grad(E)=71.910 E(BOND)=2078.473 E(ANGL)=15665.773 | | E(VDW )=2917.673 E(CDIH)=3634.409 E(NOE )=21685.630 E(PLAN)=647.245 | ------------------------------------------------------------------------------- NBONDS: found 14899 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =44519.576 grad(E)=59.704 E(BOND)=1778.618 E(ANGL)=14077.073 | | E(VDW )=2779.366 E(CDIH)=3576.445 E(NOE )=21673.750 E(PLAN)=634.324 | ------------------------------------------------------------------------------- NBONDS: found 14803 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =42042.470 grad(E)=67.125 E(BOND)=1670.837 E(ANGL)=12573.896 | | E(VDW )=2691.502 E(CDIH)=3456.780 E(NOE )=21011.105 E(PLAN)=638.350 | ------------------------------------------------------------------------------- NBONDS: found 14723 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =40433.978 grad(E)=43.878 E(BOND)=1512.765 E(ANGL)=11973.585 | | E(VDW )=2538.526 E(CDIH)=3464.320 E(NOE )=20295.992 E(PLAN)=648.790 | ------------------------------------------------------------------------------- NBONDS: found 14575 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =38915.185 grad(E)=46.834 E(BOND)=1461.281 E(ANGL)=11546.789 | | E(VDW )=2210.891 E(CDIH)=3447.171 E(NOE )=19592.787 E(PLAN)=656.265 | ------------------------------------------------------------------------------- NBONDS: found 14452 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =37732.983 grad(E)=40.472 E(BOND)=1331.285 E(ANGL)=11314.702 | | E(VDW )=1948.072 E(CDIH)=3338.013 E(NOE )=19125.174 E(PLAN)=675.739 | ------------------------------------------------------------------------------- NBONDS: found 14313 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0001 ----------------------- | Etotal =36793.986 grad(E)=39.356 E(BOND)=1202.459 E(ANGL)=11013.388 | | E(VDW )=1750.845 E(CDIH)=3289.070 E(NOE )=18876.860 E(PLAN)=661.363 | ------------------------------------------------------------------------------- NBONDS: found 14198 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0001 ----------------------- | Etotal =35785.166 grad(E)=46.381 E(BOND)=1187.224 E(ANGL)=10768.772 | | E(VDW )=1637.846 E(CDIH)=3251.124 E(NOE )=18347.340 E(PLAN)=592.859 | ------------------------------------------------------------------------------- NBONDS: found 14082 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0001 ----------------------- | Etotal =34954.378 grad(E)=35.144 E(BOND)=1119.371 E(ANGL)=10584.151 | | E(VDW )=1588.291 E(CDIH)=3194.946 E(NOE )=17948.752 E(PLAN)=518.868 | ------------------------------------------------------------------------------- NBONDS: found 13949 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0001 ----------------------- | Etotal =34382.779 grad(E)=33.574 E(BOND)=1116.431 E(ANGL)=10322.260 | | E(VDW )=1511.831 E(CDIH)=3212.963 E(NOE )=17762.600 E(PLAN)=456.695 | ------------------------------------------------------------------------------- NBONDS: found 13810 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =33771.957 grad(E)=33.049 E(BOND)=1095.353 E(ANGL)=10090.280 | | E(VDW )=1400.915 E(CDIH)=3187.168 E(NOE )=17603.501 E(PLAN)=394.739 | ------------------------------------------------------------------------------- NBONDS: found 13712 intra-atom interactions --------------- cycle= 160 ------ stepsize= 0.0001 ----------------------- | Etotal =33236.392 grad(E)=31.829 E(BOND)=1080.622 E(ANGL)=9859.323 | | E(VDW )=1335.954 E(CDIH)=3124.752 E(NOE )=17483.099 E(PLAN)=352.643 | ------------------------------------------------------------------------------- --------------- cycle= 170 ------ stepsize= 0.0001 ----------------------- | Etotal =32894.092 grad(E)=27.189 E(BOND)=1033.982 E(ANGL)=9659.198 | | E(VDW )=1256.903 E(CDIH)=3104.477 E(NOE )=17502.023 E(PLAN)=337.508 | ------------------------------------------------------------------------------- NBONDS: found 13551 intra-atom interactions --------------- cycle= 180 ------ stepsize= 0.0001 ----------------------- | Etotal =32616.384 grad(E)=23.798 E(BOND)=1028.013 E(ANGL)=9571.603 | | E(VDW )=1192.256 E(CDIH)=3071.570 E(NOE )=17425.012 E(PLAN)=327.930 | ------------------------------------------------------------------------------- NBONDS: found 13418 intra-atom interactions --------------- cycle= 190 ------ stepsize= 0.0001 ----------------------- | Etotal =32291.062 grad(E)=22.279 E(BOND)=997.197 E(ANGL)=9498.338 | | E(VDW )=1139.767 E(CDIH)=3032.109 E(NOE )=17294.891 E(PLAN)=328.760 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =31944.849 grad(E)=23.544 E(BOND)=973.362 E(ANGL)=9266.760 | | E(VDW )=1111.300 E(CDIH)=3017.522 E(NOE )=17227.338 E(PLAN)=348.568 | ------------------------------------------------------------------------------- NBONDS: found 13316 intra-atom interactions --------------- cycle= 210 ------ stepsize= 0.0001 ----------------------- | Etotal =31488.604 grad(E)=27.080 E(BOND)=914.411 E(ANGL)=8792.273 | | E(VDW )=1128.987 E(CDIH)=3002.998 E(NOE )=17285.593 E(PLAN)=364.342 | ------------------------------------------------------------------------------- NBONDS: found 13292 intra-atom interactions --------------- cycle= 220 ------ stepsize= 0.0001 ----------------------- | Etotal =30989.664 grad(E)=28.081 E(BOND)=914.561 E(ANGL)=8362.278 | | E(VDW )=1119.932 E(CDIH)=3046.248 E(NOE )=17185.569 E(PLAN)=361.077 | ------------------------------------------------------------------------------- NBONDS: found 13204 intra-atom interactions --------------- cycle= 230 ------ stepsize= 0.0001 ----------------------- | Etotal =30509.772 grad(E)=26.143 E(BOND)=965.682 E(ANGL)=7984.431 | | E(VDW )=1141.336 E(CDIH)=3101.881 E(NOE )=16958.634 E(PLAN)=357.807 | ------------------------------------------------------------------------------- NBONDS: found 13146 intra-atom interactions --------------- cycle= 240 ------ stepsize= 0.0001 ----------------------- | Etotal =30058.073 grad(E)=24.244 E(BOND)=937.516 E(ANGL)=7675.150 | | E(VDW )=1103.609 E(CDIH)=3145.082 E(NOE )=16842.438 E(PLAN)=354.278 | ------------------------------------------------------------------------------- NBONDS: found 13073 intra-atom interactions --------------- cycle= 250 ------ stepsize= 0.0001 ----------------------- | Etotal =29670.883 grad(E)=28.525 E(BOND)=955.715 E(ANGL)=7501.268 | | E(VDW )=1056.650 E(CDIH)=3176.873 E(NOE )=16639.376 E(PLAN)=341.001 | ------------------------------------------------------------------------------- NBONDS: found 13042 intra-atom interactions --------------- cycle= 260 ------ stepsize= 0.0001 ----------------------- | Etotal =29258.228 grad(E)=23.568 E(BOND)=935.408 E(ANGL)=7312.176 | | E(VDW )=1019.791 E(CDIH)=3178.363 E(NOE )=16482.088 E(PLAN)=330.403 | ------------------------------------------------------------------------------- NBONDS: found 12991 intra-atom interactions --------------- cycle= 270 ------ stepsize= 0.0001 ----------------------- | Etotal =28980.457 grad(E)=18.623 E(BOND)=913.069 E(ANGL)=7302.231 | | E(VDW )=936.984 E(CDIH)=3126.266 E(NOE )=16369.129 E(PLAN)=332.778 | ------------------------------------------------------------------------------- --------------- cycle= 280 ------ stepsize= 0.0001 ----------------------- | Etotal =28697.002 grad(E)=17.842 E(BOND)=902.419 E(ANGL)=7272.286 | | E(VDW )=864.887 E(CDIH)=3081.118 E(NOE )=16241.853 E(PLAN)=334.440 | ------------------------------------------------------------------------------- NBONDS: found 12919 intra-atom interactions --------------- cycle= 290 ------ stepsize= 0.0001 ----------------------- | Etotal =28421.484 grad(E)=19.669 E(BOND)=868.496 E(ANGL)=7159.706 | | E(VDW )=836.722 E(CDIH)=3056.486 E(NOE )=16157.002 E(PLAN)=343.072 | ------------------------------------------------------------------------------- NBONDS: found 12855 intra-atom interactions --------------- cycle= 300 ------ stepsize= 0.0001 ----------------------- | Etotal =28202.355 grad(E)=19.080 E(BOND)=871.061 E(ANGL)=7116.307 | | E(VDW )=783.048 E(CDIH)=3038.051 E(NOE )=16047.647 E(PLAN)=346.241 | ------------------------------------------------------------------------------- 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= 511252417. ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 0.00000 0.00001 0.00001 velocity [A/ps] : -0.10104 0.15737 0.03031 ang. mom. [amu A/ps] : -42795.54181 218114.23102 -12000.60521 kin. ener. [Kcal/mol] : 2.90390 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00000 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 12847 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=37956.531 E(kin)=6169.733 temperature=3057.362 | | Etotal =31786.798 grad(E)=84.772 E(BOND)=87.106 E(ANGL)=711.631 | | E(DIHE)=0.000 E(IMPR)=10773.075 E(VDW )=783.048 E(CDIH)=3038.051 | | E(NOE )=16047.647 E(PLAN)=346.241 | ------------------------------------------------------------------------------- NBONDS: found 12792 intra-atom interactions NBONDS: found 12773 intra-atom interactions NBONDS: found 12806 intra-atom interactions NBONDS: found 12807 intra-atom interactions NBONDS: found 12796 intra-atom interactions NBONDS: found 12808 intra-atom interactions NBONDS: found 12806 intra-atom interactions NBONDS: found 12817 intra-atom interactions NBONDS: found 12784 intra-atom interactions NBONDS: found 12777 intra-atom interactions NBONDS: found 12744 intra-atom interactions NBONDS: found 12731 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=33382.913 E(kin)=7503.727 temperature=3718.412 | | Etotal =25879.186 grad(E)=73.890 E(BOND)=2938.065 E(ANGL)=5129.014 | | E(DIHE)=0.000 E(IMPR)=4794.527 E(VDW )=621.226 E(CDIH)=2001.356 | | E(NOE )=10072.538 E(PLAN)=322.460 | ------------------------------------------------------------------------------- NBONDS: found 12709 intra-atom interactions NBONDS: found 12719 intra-atom interactions NBONDS: found 12715 intra-atom interactions NBONDS: found 12705 intra-atom interactions NBONDS: found 12657 intra-atom interactions NBONDS: found 12633 intra-atom interactions NBONDS: found 12628 intra-atom interactions NBONDS: found 12617 intra-atom interactions NBONDS: found 12599 intra-atom interactions NBONDS: found 12582 intra-atom interactions NBONDS: found 12562 intra-atom interactions NBONDS: found 12541 intra-atom interactions NBONDS: found 12507 intra-atom interactions NBONDS: found 12470 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=28833.839 E(kin)=7024.749 temperature=3481.058 | | Etotal =21809.090 grad(E)=69.848 E(BOND)=2660.978 E(ANGL)=4668.989 | | E(DIHE)=0.000 E(IMPR)=4206.773 E(VDW )=623.314 E(CDIH)=1777.339 | | E(NOE )=7638.275 E(PLAN)=233.421 | ------------------------------------------------------------------------------- NBONDS: found 12420 intra-atom interactions NBONDS: found 12412 intra-atom interactions NBONDS: found 12330 intra-atom interactions NBONDS: found 12233 intra-atom interactions NBONDS: found 12122 intra-atom interactions NBONDS: found 12060 intra-atom interactions NBONDS: found 12004 intra-atom interactions NBONDS: found 11961 intra-atom interactions NBONDS: found 11900 intra-atom interactions NBONDS: found 11880 intra-atom interactions NBONDS: found 11836 intra-atom interactions NBONDS: found 11827 intra-atom interactions NBONDS: found 11804 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=26586.864 E(kin)=7065.403 temperature=3501.204 | | Etotal =19521.461 grad(E)=66.462 E(BOND)=2795.814 E(ANGL)=4259.304 | | E(DIHE)=0.000 E(IMPR)=3935.813 E(VDW )=326.454 E(CDIH)=1470.260 | | E(NOE )=6649.069 E(PLAN)=84.746 | ------------------------------------------------------------------------------- NBONDS: found 11801 intra-atom interactions NBONDS: found 11830 intra-atom interactions NBONDS: found 11853 intra-atom interactions NBONDS: found 11873 intra-atom interactions NBONDS: found 11891 intra-atom interactions NBONDS: found 11840 intra-atom interactions NBONDS: found 11791 intra-atom interactions NBONDS: found 11726 intra-atom interactions NBONDS: found 11719 intra-atom interactions NBONDS: found 11692 intra-atom interactions NBONDS: found 11668 intra-atom interactions NBONDS: found 11626 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=25263.198 E(kin)=6566.785 temperature=3254.118 | | Etotal =18696.413 grad(E)=66.344 E(BOND)=2578.148 E(ANGL)=4303.313 | | E(DIHE)=0.000 E(IMPR)=3554.613 E(VDW )=474.281 E(CDIH)=1381.563 | | E(NOE )=6289.360 E(PLAN)=115.135 | ------------------------------------------------------------------------------- NBONDS: found 11595 intra-atom interactions NBONDS: found 11530 intra-atom interactions NBONDS: found 11480 intra-atom interactions NBONDS: found 11421 intra-atom interactions NBONDS: found 11382 intra-atom interactions NBONDS: found 11357 intra-atom interactions NBONDS: found 11316 intra-atom interactions NBONDS: found 11283 intra-atom interactions NBONDS: found 11267 intra-atom interactions NBONDS: found 11282 intra-atom interactions NBONDS: found 11239 intra-atom interactions NBONDS: found 11202 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=24102.577 E(kin)=6508.014 temperature=3224.994 | | Etotal =17594.563 grad(E)=65.569 E(BOND)=2342.572 E(ANGL)=4095.456 | | E(DIHE)=0.000 E(IMPR)=3352.059 E(VDW )=331.510 E(CDIH)=1082.447 | | E(NOE )=6313.131 E(PLAN)=77.388 | ------------------------------------------------------------------------------- NBONDS: found 11183 intra-atom interactions NBONDS: found 11173 intra-atom interactions NBONDS: found 11175 intra-atom interactions NBONDS: found 11156 intra-atom interactions NBONDS: found 11159 intra-atom interactions NBONDS: found 11208 intra-atom interactions NBONDS: found 11217 intra-atom interactions NBONDS: found 11201 intra-atom interactions NBONDS: found 11192 intra-atom interactions NBONDS: found 11177 intra-atom interactions NBONDS: found 11192 intra-atom interactions NBONDS: found 11146 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=23008.135 E(kin)=6169.574 temperature=3057.283 | | Etotal =16838.560 grad(E)=66.887 E(BOND)=2628.322 E(ANGL)=3804.120 | | E(DIHE)=0.000 E(IMPR)=3490.440 E(VDW )=283.175 E(CDIH)=654.413 | | E(NOE )=5852.523 E(PLAN)=125.567 | ------------------------------------------------------------------------------- NBONDS: found 11127 intra-atom interactions NBONDS: found 11127 intra-atom interactions NBONDS: found 11164 intra-atom interactions NBONDS: found 11181 intra-atom interactions NBONDS: found 11199 intra-atom interactions NBONDS: found 11265 intra-atom interactions NBONDS: found 11242 intra-atom interactions NBONDS: found 11227 intra-atom interactions NBONDS: found 11226 intra-atom interactions NBONDS: found 11269 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=22897.236 E(kin)=6292.731 temperature=3118.313 | | Etotal =16604.505 grad(E)=67.552 E(BOND)=2314.123 E(ANGL)=3745.343 | | E(DIHE)=0.000 E(IMPR)=3358.051 E(VDW )=350.800 E(CDIH)=645.429 | | E(NOE )=6090.823 E(PLAN)=99.934 | ------------------------------------------------------------------------------- NBONDS: found 11232 intra-atom interactions NBONDS: found 11232 intra-atom interactions NBONDS: found 11223 intra-atom interactions NBONDS: found 11210 intra-atom interactions NBONDS: found 11187 intra-atom interactions NBONDS: found 11199 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00000 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] : 0.00000 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] : 0.00000 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 11199 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=31988.478 E(kin)=6197.669 temperature=3071.205 | | Etotal =25790.809 grad(E)=124.672 E(BOND)=4601.699 E(ANGL)=7417.814 | | E(DIHE)=0.000 E(IMPR)=6559.883 E(VDW )=302.062 E(CDIH)=699.126 | | E(NOE )=6098.876 E(PLAN)=111.349 | ------------------------------------------------------------------------------- NBONDS: found 11201 intra-atom interactions NBONDS: found 11260 intra-atom interactions NBONDS: found 11249 intra-atom interactions NBONDS: found 11254 intra-atom interactions NBONDS: found 11264 intra-atom interactions NBONDS: found 11334 intra-atom interactions NBONDS: found 11346 intra-atom interactions NBONDS: found 11396 intra-atom interactions NBONDS: found 11446 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=27327.957 E(kin)=6654.894 temperature=3297.779 | | Etotal =20673.063 grad(E)=100.131 E(BOND)=2810.192 E(ANGL)=4701.323 | | E(DIHE)=0.000 E(IMPR)=5007.241 E(VDW )=297.528 E(CDIH)=964.971 | | E(NOE )=6715.323 E(PLAN)=176.485 | ------------------------------------------------------------------------------- NBONDS: found 11433 intra-atom interactions NBONDS: found 11433 intra-atom interactions NBONDS: found 11420 intra-atom interactions NBONDS: found 11475 intra-atom interactions NBONDS: found 11441 intra-atom interactions NBONDS: found 11475 intra-atom interactions NBONDS: found 11487 intra-atom interactions NBONDS: found 11508 intra-atom interactions NBONDS: found 11501 intra-atom interactions NBONDS: found 11527 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=26474.389 E(kin)=6287.982 temperature=3115.959 | | Etotal =20186.407 grad(E)=94.947 E(BOND)=2610.757 E(ANGL)=4852.937 | | E(DIHE)=0.000 E(IMPR)=4765.241 E(VDW )=315.567 E(CDIH)=841.062 | | E(NOE )=6642.098 E(PLAN)=158.744 | ------------------------------------------------------------------------------- NBONDS: found 11502 intra-atom interactions NBONDS: found 11556 intra-atom interactions NBONDS: found 11555 intra-atom interactions NBONDS: found 11540 intra-atom interactions NBONDS: found 11492 intra-atom interactions NBONDS: found 11463 intra-atom interactions NBONDS: found 11467 intra-atom interactions NBONDS: found 11489 intra-atom interactions NBONDS: found 11517 intra-atom interactions NBONDS: found 11536 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=25650.264 E(kin)=6103.922 temperature=3024.750 | | Etotal =19546.342 grad(E)=89.464 E(BOND)=2465.106 E(ANGL)=4363.478 | | E(DIHE)=0.000 E(IMPR)=4728.943 E(VDW )=306.115 E(CDIH)=822.788 | | E(NOE )=6705.189 E(PLAN)=154.722 | ------------------------------------------------------------------------------- NBONDS: found 11601 intra-atom interactions NBONDS: found 11631 intra-atom interactions NBONDS: found 11651 intra-atom interactions NBONDS: found 11612 intra-atom interactions NBONDS: found 11619 intra-atom interactions NBONDS: found 11584 intra-atom interactions NBONDS: found 11590 intra-atom interactions NBONDS: found 11626 intra-atom interactions NBONDS: found 11657 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=25232.661 E(kin)=5933.806 temperature=2940.450 | | Etotal =19298.855 grad(E)=89.849 E(BOND)=2443.813 E(ANGL)=4308.078 | | E(DIHE)=0.000 E(IMPR)=4584.670 E(VDW )=321.930 E(CDIH)=914.426 | | E(NOE )=6598.750 E(PLAN)=127.189 | ------------------------------------------------------------------------------- NBONDS: found 11689 intra-atom interactions NBONDS: found 11717 intra-atom interactions NBONDS: found 11687 intra-atom interactions NBONDS: found 11783 intra-atom interactions NBONDS: found 11821 intra-atom interactions NBONDS: found 11891 intra-atom interactions NBONDS: found 11921 intra-atom interactions NBONDS: found 11942 intra-atom interactions NBONDS: found 11945 intra-atom interactions NBONDS: found 11995 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=25242.601 E(kin)=6054.442 temperature=3000.230 | | Etotal =19188.158 grad(E)=85.570 E(BOND)=2225.754 E(ANGL)=4597.053 | | E(DIHE)=0.000 E(IMPR)=4677.472 E(VDW )=365.056 E(CDIH)=898.371 | | E(NOE )=6326.853 E(PLAN)=97.600 | ------------------------------------------------------------------------------- NBONDS: found 11984 intra-atom interactions NBONDS: found 11978 intra-atom interactions NBONDS: found 11986 intra-atom interactions NBONDS: found 12004 intra-atom interactions NBONDS: found 11998 intra-atom interactions NBONDS: found 11997 intra-atom interactions NBONDS: found 12048 intra-atom interactions NBONDS: found 12054 intra-atom interactions NBONDS: found 12092 intra-atom interactions NBONDS: found 12087 intra-atom interactions NBONDS: found 12102 intra-atom interactions NBONDS: found 12111 intra-atom interactions NBONDS: found 12062 intra-atom interactions NBONDS: found 12062 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=25957.370 E(kin)=5855.048 temperature=2901.422 | | Etotal =20102.322 grad(E)=95.994 E(BOND)=2880.202 E(ANGL)=4389.616 | | E(DIHE)=0.000 E(IMPR)=4854.766 E(VDW )=462.329 E(CDIH)=906.806 | | E(NOE )=6485.068 E(PLAN)=123.535 | ------------------------------------------------------------------------------- NBONDS: found 12012 intra-atom interactions NBONDS: found 12014 intra-atom interactions NBONDS: found 12018 intra-atom interactions NBONDS: found 12006 intra-atom interactions NBONDS: found 12001 intra-atom interactions NBONDS: found 12005 intra-atom interactions NBONDS: found 12032 intra-atom interactions NBONDS: found 12031 intra-atom interactions NBONDS: found 12038 intra-atom interactions NBONDS: found 12034 intra-atom interactions NBONDS: found 12054 intra-atom interactions NBONDS: found 12045 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=25522.012 E(kin)=6228.603 temperature=3086.534 | | Etotal =19293.409 grad(E)=94.346 E(BOND)=2557.271 E(ANGL)=4530.968 | | E(DIHE)=0.000 E(IMPR)=4572.022 E(VDW )=309.372 E(CDIH)=882.272 | | E(NOE )=6311.844 E(PLAN)=129.659 | ------------------------------------------------------------------------------- NBONDS: found 12089 intra-atom interactions NBONDS: found 12123 intra-atom interactions NBONDS: found 12127 intra-atom interactions NBONDS: found 12147 intra-atom interactions NBONDS: found 12132 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00000 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] : 0.00000 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] : 0.00000 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 12136 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=30164.399 E(kin)=6269.777 temperature=3106.938 | | Etotal =23894.622 grad(E)=102.753 E(BOND)=2538.248 E(ANGL)=4032.314 | | E(DIHE)=0.000 E(IMPR)=9487.691 E(VDW )=352.196 E(CDIH)=890.713 | | E(NOE )=6441.553 E(PLAN)=151.907 | ------------------------------------------------------------------------------- NBONDS: found 12152 intra-atom interactions NBONDS: found 12195 intra-atom interactions NBONDS: found 12220 intra-atom interactions NBONDS: found 12275 intra-atom interactions NBONDS: found 12320 intra-atom interactions NBONDS: found 12323 intra-atom interactions NBONDS: found 12425 intra-atom interactions NBONDS: found 12511 intra-atom interactions NBONDS: found 12554 intra-atom interactions NBONDS: found 12653 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=27986.928 E(kin)=6776.718 temperature=3358.148 | | Etotal =21210.210 grad(E)=100.227 E(BOND)=2828.956 E(ANGL)=6038.501 | | E(DIHE)=0.000 E(IMPR)=3282.426 E(VDW )=406.648 E(CDIH)=1331.466 | | E(NOE )=7083.771 E(PLAN)=238.443 | ------------------------------------------------------------------------------- NBONDS: found 12698 intra-atom interactions NBONDS: found 12766 intra-atom interactions NBONDS: found 12848 intra-atom interactions NBONDS: found 12883 intra-atom interactions NBONDS: found 12953 intra-atom interactions NBONDS: found 12975 intra-atom interactions NBONDS: found 13004 intra-atom interactions NBONDS: found 13038 intra-atom interactions NBONDS: found 13068 intra-atom interactions NBONDS: found 13118 intra-atom interactions NBONDS: found 13165 intra-atom interactions NBONDS: found 13235 intra-atom interactions NBONDS: found 13280 intra-atom interactions NBONDS: found 13352 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=26154.888 E(kin)=6171.839 temperature=3058.405 | | Etotal =19983.049 grad(E)=95.455 E(BOND)=2618.336 E(ANGL)=5441.680 | | E(DIHE)=0.000 E(IMPR)=2269.857 E(VDW )=447.874 E(CDIH)=1585.280 | | E(NOE )=7382.113 E(PLAN)=237.908 | ------------------------------------------------------------------------------- NBONDS: found 13396 intra-atom interactions NBONDS: found 13479 intra-atom interactions NBONDS: found 13560 intra-atom interactions NBONDS: found 13639 intra-atom interactions NBONDS: found 13678 intra-atom interactions NBONDS: found 13738 intra-atom interactions NBONDS: found 13785 intra-atom interactions NBONDS: found 13905 intra-atom interactions NBONDS: found 13913 intra-atom interactions NBONDS: found 13924 intra-atom interactions NBONDS: found 13922 intra-atom interactions NBONDS: found 13923 intra-atom interactions NBONDS: found 13920 intra-atom interactions NBONDS: found 13920 intra-atom interactions NBONDS: found 13956 intra-atom interactions NBONDS: found 13966 intra-atom interactions NBONDS: found 13958 intra-atom interactions NBONDS: found 13956 intra-atom interactions NBONDS: found 13963 intra-atom interactions NBONDS: found 13981 intra-atom interactions NBONDS: found 13982 intra-atom interactions NBONDS: found 13996 intra-atom interactions NBONDS: found 13995 intra-atom interactions NBONDS: found 14021 intra-atom interactions NBONDS: found 14048 intra-atom interactions NBONDS: found 14042 intra-atom interactions NBONDS: found 14049 intra-atom interactions NBONDS: found 14033 intra-atom interactions NBONDS: found 14016 intra-atom interactions NBONDS: found 14002 intra-atom interactions NBONDS: found 14004 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=35814.755 E(kin)=11759.902 temperature=5827.525 | | Etotal =24054.854 grad(E)=128.846 E(BOND)=5153.093 E(ANGL)=6712.719 | | E(DIHE)=0.000 E(IMPR)=2245.601 E(VDW )=464.542 E(CDIH)=1850.729 | | E(NOE )=7354.681 E(PLAN)=273.489 | ------------------------------------------------------------------------------- NBONDS: found 13988 intra-atom interactions NBONDS: found 13975 intra-atom interactions NBONDS: found 13991 intra-atom interactions NBONDS: found 13972 intra-atom interactions NBONDS: found 13986 intra-atom interactions NBONDS: found 13984 intra-atom interactions NBONDS: found 14008 intra-atom interactions NBONDS: found 13992 intra-atom interactions NBONDS: found 14014 intra-atom interactions NBONDS: found 14004 intra-atom interactions NBONDS: found 14000 intra-atom interactions NBONDS: found 13998 intra-atom interactions NBONDS: found 14020 intra-atom interactions NBONDS: found 14016 intra-atom interactions NBONDS: found 14003 intra-atom interactions NBONDS: found 14010 intra-atom interactions NBONDS: found 13977 intra-atom interactions NBONDS: found 13978 intra-atom interactions NBONDS: found 13949 intra-atom interactions NBONDS: found 13974 intra-atom interactions NBONDS: found 13984 intra-atom interactions NBONDS: found 14016 intra-atom interactions NBONDS: found 14066 intra-atom interactions NBONDS: found 14043 intra-atom interactions NBONDS: found 14028 intra-atom interactions NBONDS: found 14048 intra-atom interactions NBONDS: found 14057 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=27188.517 E(kin)=6315.850 temperature=3129.769 | | Etotal =20872.667 grad(E)=112.919 E(BOND)=3474.175 E(ANGL)=6304.959 | | E(DIHE)=0.000 E(IMPR)=1674.009 E(VDW )=471.738 E(CDIH)=1353.383 | | E(NOE )=7345.906 E(PLAN)=248.497 | ------------------------------------------------------------------------------- NBONDS: found 14080 intra-atom interactions NBONDS: found 14088 intra-atom interactions NBONDS: found 14124 intra-atom interactions NBONDS: found 14154 intra-atom interactions NBONDS: found 14204 intra-atom interactions NBONDS: found 14250 intra-atom interactions NBONDS: found 14248 intra-atom interactions NBONDS: found 14243 intra-atom interactions NBONDS: found 14247 intra-atom interactions NBONDS: found 14250 intra-atom interactions NBONDS: found 14243 intra-atom interactions NBONDS: found 14238 intra-atom interactions NBONDS: found 14229 intra-atom interactions NBONDS: found 14260 intra-atom interactions NBONDS: found 14258 intra-atom interactions NBONDS: found 14222 intra-atom interactions NBONDS: found 14228 intra-atom interactions NBONDS: found 14209 intra-atom interactions NBONDS: found 14212 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=25890.192 E(kin)=6456.827 temperature=3199.629 | | Etotal =19433.365 grad(E)=90.678 E(BOND)=2888.865 E(ANGL)=5091.680 | | E(DIHE)=0.000 E(IMPR)=1594.906 E(VDW )=488.526 E(CDIH)=1371.284 | | E(NOE )=7771.280 E(PLAN)=226.825 | ------------------------------------------------------------------------------- NBONDS: found 14245 intra-atom interactions NBONDS: found 14297 intra-atom interactions NBONDS: found 14305 intra-atom interactions NBONDS: found 14289 intra-atom interactions NBONDS: found 14306 intra-atom interactions NBONDS: found 14324 intra-atom interactions NBONDS: found 14305 intra-atom interactions NBONDS: found 14334 intra-atom interactions NBONDS: found 14313 intra-atom interactions NBONDS: found 14321 intra-atom interactions NBONDS: found 14381 intra-atom interactions NBONDS: found 14401 intra-atom interactions NBONDS: found 14408 intra-atom interactions NBONDS: found 14407 intra-atom interactions NBONDS: found 14398 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=26070.275 E(kin)=5899.888 temperature=2923.642 | | Etotal =20170.387 grad(E)=106.305 E(BOND)=3069.639 E(ANGL)=5490.012 | | E(DIHE)=0.000 E(IMPR)=1752.663 E(VDW )=498.972 E(CDIH)=1239.468 | | E(NOE )=7908.032 E(PLAN)=211.602 | ------------------------------------------------------------------------------- NBONDS: found 14364 intra-atom interactions NBONDS: found 14371 intra-atom interactions NBONDS: found 14364 intra-atom interactions NBONDS: found 14268 intra-atom interactions NBONDS: found 14253 intra-atom interactions NBONDS: found 14243 intra-atom interactions NBONDS: found 14240 intra-atom interactions NBONDS: found 14235 intra-atom interactions NBONDS: found 14264 intra-atom interactions NBONDS: found 14229 intra-atom interactions NBONDS: found 14209 intra-atom interactions NBONDS: found 14222 intra-atom interactions NBONDS: found 14235 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=25823.481 E(kin)=5882.481 temperature=2915.017 | | Etotal =19941.000 grad(E)=98.856 E(BOND)=2933.547 E(ANGL)=5444.069 | | E(DIHE)=0.000 E(IMPR)=1916.621 E(VDW )=491.788 E(CDIH)=1354.023 | | E(NOE )=7572.745 E(PLAN)=228.207 | ------------------------------------------------------------------------------- NBONDS: found 14239 intra-atom interactions NBONDS: found 14243 intra-atom interactions NBONDS: found 14308 intra-atom interactions NBONDS: found 14337 intra-atom interactions NBONDS: found 14364 intra-atom interactions NBONDS: found 14360 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00000 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] : 0.00000 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] : 0.00000 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 13066 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=35175.815 E(kin)=6352.361 temperature=3147.862 | | Etotal =28823.454 grad(E)=176.404 E(BOND)=5811.227 E(ANGL)=9983.644 | | E(DIHE)=0.000 E(IMPR)=4219.225 E(VDW )=95.063 E(CDIH)=1387.871 | | E(NOE )=7124.645 E(PLAN)=201.778 | ------------------------------------------------------------------------------- NBONDS: found 13066 intra-atom interactions NBONDS: found 13061 intra-atom interactions NBONDS: found 13036 intra-atom interactions NBONDS: found 13071 intra-atom interactions NBONDS: found 13147 intra-atom interactions NBONDS: found 13149 intra-atom interactions NBONDS: found 13178 intra-atom interactions NBONDS: found 13187 intra-atom interactions NBONDS: found 13163 intra-atom interactions NBONDS: found 13135 intra-atom interactions NBONDS: found 13128 intra-atom interactions NBONDS: found 13138 intra-atom interactions NBONDS: found 13130 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=30409.395 E(kin)=6307.655 temperature=3125.708 | | Etotal =24101.740 grad(E)=137.945 E(BOND)=3067.749 E(ANGL)=7016.652 | | E(DIHE)=0.000 E(IMPR)=2392.739 E(VDW )=99.753 E(CDIH)=1678.226 | | E(NOE )=9549.668 E(PLAN)=296.953 | ------------------------------------------------------------------------------- NBONDS: found 13115 intra-atom interactions NBONDS: found 13108 intra-atom interactions NBONDS: found 13157 intra-atom interactions NBONDS: found 13194 intra-atom interactions NBONDS: found 13188 intra-atom interactions NBONDS: found 13212 intra-atom interactions NBONDS: found 13240 intra-atom interactions NBONDS: found 13236 intra-atom interactions NBONDS: found 13296 intra-atom interactions NBONDS: found 13272 intra-atom interactions NBONDS: found 13237 intra-atom interactions NBONDS: found 13241 intra-atom interactions NBONDS: found 13235 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=32089.821 E(kin)=7559.072 temperature=3745.838 | | Etotal =24530.749 grad(E)=138.098 E(BOND)=3218.310 E(ANGL)=7472.966 | | E(DIHE)=0.000 E(IMPR)=1921.128 E(VDW )=102.922 E(CDIH)=1539.683 | | E(NOE )=9854.764 E(PLAN)=420.977 | ------------------------------------------------------------------------------- NBONDS: found 13246 intra-atom interactions NBONDS: found 13249 intra-atom interactions NBONDS: found 13255 intra-atom interactions NBONDS: found 13270 intra-atom interactions NBONDS: found 13253 intra-atom interactions NBONDS: found 13251 intra-atom interactions NBONDS: found 13235 intra-atom interactions NBONDS: found 13208 intra-atom interactions NBONDS: found 13188 intra-atom interactions NBONDS: found 13196 intra-atom interactions NBONDS: found 13221 intra-atom interactions NBONDS: found 13209 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=29747.060 E(kin)=6501.585 temperature=3221.808 | | Etotal =23245.475 grad(E)=133.853 E(BOND)=2967.988 E(ANGL)=7153.726 | | E(DIHE)=0.000 E(IMPR)=2011.321 E(VDW )=101.418 E(CDIH)=1508.428 | | E(NOE )=9192.821 E(PLAN)=309.773 | ------------------------------------------------------------------------------- NBONDS: found 13227 intra-atom interactions NBONDS: found 13238 intra-atom interactions NBONDS: found 13246 intra-atom interactions NBONDS: found 13269 intra-atom interactions NBONDS: found 13226 intra-atom interactions NBONDS: found 13235 intra-atom interactions NBONDS: found 13195 intra-atom interactions NBONDS: found 13183 intra-atom interactions NBONDS: found 13223 intra-atom interactions NBONDS: found 13284 intra-atom interactions NBONDS: found 13345 intra-atom interactions NBONDS: found 13444 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=29496.430 E(kin)=6385.595 temperature=3164.330 | | Etotal =23110.835 grad(E)=127.796 E(BOND)=3042.149 E(ANGL)=6589.822 | | E(DIHE)=0.000 E(IMPR)=2151.229 E(VDW )=103.767 E(CDIH)=1709.091 | | E(NOE )=9190.730 E(PLAN)=324.046 | ------------------------------------------------------------------------------- NBONDS: found 13529 intra-atom interactions NBONDS: found 13601 intra-atom interactions NBONDS: found 13583 intra-atom interactions NBONDS: found 13602 intra-atom interactions NBONDS: found 13658 intra-atom interactions NBONDS: found 13661 intra-atom interactions NBONDS: found 13647 intra-atom interactions NBONDS: found 13631 intra-atom interactions NBONDS: found 13625 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=29436.254 E(kin)=6007.801 temperature=2977.118 | | Etotal =23428.453 grad(E)=134.212 E(BOND)=3057.583 E(ANGL)=7355.230 | | E(DIHE)=0.000 E(IMPR)=2280.797 E(VDW )=108.189 E(CDIH)=1639.103 | | E(NOE )=8628.663 E(PLAN)=358.888 | ------------------------------------------------------------------------------- NBONDS: found 13640 intra-atom interactions NBONDS: found 13574 intra-atom interactions NBONDS: found 13594 intra-atom interactions NBONDS: found 13612 intra-atom interactions NBONDS: found 13656 intra-atom interactions NBONDS: found 13654 intra-atom interactions NBONDS: found 13626 intra-atom interactions NBONDS: found 13615 intra-atom interactions NBONDS: found 13521 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=29504.226 E(kin)=6096.388 temperature=3021.016 | | Etotal =23407.838 grad(E)=132.006 E(BOND)=2845.254 E(ANGL)=6895.759 | | E(DIHE)=0.000 E(IMPR)=2245.416 E(VDW )=105.867 E(CDIH)=1494.590 | | E(NOE )=9454.030 E(PLAN)=366.922 | ------------------------------------------------------------------------------- NBONDS: found 13519 intra-atom interactions NBONDS: found 13490 intra-atom interactions NBONDS: found 13487 intra-atom interactions NBONDS: found 13470 intra-atom interactions NBONDS: found 13522 intra-atom interactions NBONDS: found 13561 intra-atom interactions NBONDS: found 13608 intra-atom interactions NBONDS: found 13698 intra-atom interactions NBONDS: found 13701 intra-atom interactions NBONDS: found 13756 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=29943.949 E(kin)=6481.431 temperature=3211.821 | | Etotal =23462.518 grad(E)=142.731 E(BOND)=3173.472 E(ANGL)=7257.150 | | E(DIHE)=0.000 E(IMPR)=2016.943 E(VDW )=106.336 E(CDIH)=1587.517 | | E(NOE )=9013.986 E(PLAN)=307.114 | ------------------------------------------------------------------------------- NBONDS: found 13740 intra-atom interactions NBONDS: found 13738 intra-atom interactions NBONDS: found 13768 intra-atom interactions NBONDS: found 13813 intra-atom interactions NBONDS: found 13843 intra-atom interactions NBONDS: found 13886 intra-atom interactions NBONDS: found 13935 intra-atom interactions NBONDS: found 13923 intra-atom interactions NBONDS: found 13944 intra-atom interactions NBONDS: found 13943 intra-atom interactions --------------- step= 800 at 1.60000 ps -------------------------------- | E(kin)+E(total)=29374.389 E(kin)=6235.258 temperature=3089.832 | | Etotal =23139.131 grad(E)=138.262 E(BOND)=2901.702 E(ANGL)=7058.034 | | E(DIHE)=0.000 E(IMPR)=2170.715 E(VDW )=111.981 E(CDIH)=1486.028 | | E(NOE )=9067.200 E(PLAN)=343.472 | ------------------------------------------------------------------------------- NBONDS: found 13956 intra-atom interactions NBONDS: found 13953 intra-atom interactions NBONDS: found 13937 intra-atom interactions NBONDS: found 13952 intra-atom interactions NBONDS: found 13937 intra-atom interactions NBONDS: found 13950 intra-atom interactions NBONDS: found 13938 intra-atom interactions NBONDS: found 13966 intra-atom interactions NBONDS: found 13979 intra-atom interactions NBONDS: found 14028 intra-atom interactions NBONDS: found 14051 intra-atom interactions NBONDS: found 14033 intra-atom interactions NBONDS: found 14015 intra-atom interactions NBONDS: found 14029 intra-atom interactions NBONDS: found 14044 intra-atom interactions NBONDS: found 14012 intra-atom interactions NBONDS: found 14040 intra-atom interactions NBONDS: found 14067 intra-atom interactions NBONDS: found 14108 intra-atom interactions --------------- step= 900 at 1.80000 ps -------------------------------- | E(kin)+E(total)=31893.239 E(kin)=7523.110 temperature=3728.017 | | Etotal =24370.129 grad(E)=145.772 E(BOND)=3030.889 E(ANGL)=7514.972 | | E(DIHE)=0.000 E(IMPR)=2926.135 E(VDW )=116.802 E(CDIH)=1175.497 | | E(NOE )=9277.289 E(PLAN)=328.546 | ------------------------------------------------------------------------------- NBONDS: found 14138 intra-atom interactions NBONDS: found 14118 intra-atom interactions NBONDS: found 14137 intra-atom interactions NBONDS: found 14194 intra-atom interactions NBONDS: found 14199 intra-atom interactions NBONDS: found 14219 intra-atom interactions NBONDS: found 14240 intra-atom interactions NBONDS: found 14281 intra-atom interactions NBONDS: found 14274 intra-atom interactions NBONDS: found 14277 intra-atom interactions NBONDS: found 14282 intra-atom interactions NBONDS: found 14235 intra-atom interactions NBONDS: found 14216 intra-atom interactions NBONDS: found 14249 intra-atom interactions NBONDS: found 14252 intra-atom interactions NBONDS: found 14258 intra-atom interactions NBONDS: found 14254 intra-atom interactions NBONDS: found 14241 intra-atom interactions NBONDS: found 14239 intra-atom interactions --------------- step= 1000 at 2.00000 ps -------------------------------- | E(kin)+E(total)=29167.150 E(kin)=6674.959 temperature=3307.723 | | Etotal =22492.190 grad(E)=146.883 E(BOND)=2961.786 E(ANGL)=5730.518 | | E(DIHE)=0.000 E(IMPR)=2119.413 E(VDW )=120.838 E(CDIH)=1122.831 | | E(NOE )=10127.355 E(PLAN)=309.450 | ------------------------------------------------------------------------------- NBONDS: found 14251 intra-atom interactions NBONDS: found 14246 intra-atom interactions NBONDS: found 14218 intra-atom interactions NBONDS: found 14246 intra-atom interactions NBONDS: found 14238 intra-atom interactions NBONDS: found 14234 intra-atom interactions NBONDS: found 14237 intra-atom interactions NBONDS: found 14277 intra-atom interactions NBONDS: found 14248 intra-atom interactions NBONDS: found 14291 intra-atom interactions NBONDS: found 14301 intra-atom interactions NBONDS: found 14324 intra-atom interactions NBONDS: found 14341 intra-atom interactions NBONDS: found 14326 intra-atom interactions NBONDS: found 14345 intra-atom interactions NBONDS: found 14374 intra-atom interactions --------------- step= 1100 at 2.20000 ps -------------------------------- | E(kin)+E(total)=27653.797 E(kin)=6147.477 temperature=3046.333 | | Etotal =21506.320 grad(E)=133.115 E(BOND)=2721.266 E(ANGL)=5594.742 | | E(DIHE)=0.000 E(IMPR)=1942.043 E(VDW )=124.928 E(CDIH)=1265.339 | | E(NOE )=9488.640 E(PLAN)=369.362 | ------------------------------------------------------------------------------- NBONDS: found 14374 intra-atom interactions NBONDS: found 14410 intra-atom interactions NBONDS: found 14415 intra-atom interactions NBONDS: found 14433 intra-atom interactions NBONDS: found 14383 intra-atom interactions NBONDS: found 14367 intra-atom interactions NBONDS: found 14365 intra-atom interactions NBONDS: found 14385 intra-atom interactions NBONDS: found 14372 intra-atom interactions NBONDS: found 14330 intra-atom interactions NBONDS: found 14359 intra-atom interactions NBONDS: found 14324 intra-atom interactions NBONDS: found 14306 intra-atom interactions NBONDS: found 14309 intra-atom interactions --------------- step= 1200 at 2.40000 ps -------------------------------- | E(kin)+E(total)=27255.357 E(kin)=5961.488 temperature=2954.167 | | Etotal =21293.870 grad(E)=130.268 E(BOND)=2725.144 E(ANGL)=5612.410 | | E(DIHE)=0.000 E(IMPR)=1800.155 E(VDW )=126.734 E(CDIH)=1170.902 | | E(NOE )=9496.773 E(PLAN)=361.751 | ------------------------------------------------------------------------------- NBONDS: found 14345 intra-atom interactions NBONDS: found 14327 intra-atom interactions NBONDS: found 14332 intra-atom interactions NBONDS: found 14392 intra-atom interactions NBONDS: found 14431 intra-atom interactions NBONDS: found 14452 intra-atom interactions NBONDS: found 14471 intra-atom interactions NBONDS: found 14491 intra-atom interactions NBONDS: found 14519 intra-atom interactions NBONDS: found 14542 intra-atom interactions NBONDS: found 14566 intra-atom interactions NBONDS: found 14595 intra-atom interactions NBONDS: found 14684 intra-atom interactions --------------- step= 1300 at 2.60000 ps -------------------------------- | E(kin)+E(total)=26986.423 E(kin)=6107.169 temperature=3026.359 | | Etotal =20879.254 grad(E)=129.091 E(BOND)=2586.594 E(ANGL)=5522.613 | | E(DIHE)=0.000 E(IMPR)=1884.383 E(VDW )=136.021 E(CDIH)=1050.745 | | E(NOE )=9309.653 E(PLAN)=389.244 | ------------------------------------------------------------------------------- NBONDS: found 14736 intra-atom interactions NBONDS: found 14712 intra-atom interactions NBONDS: found 14790 intra-atom interactions NBONDS: found 14836 intra-atom interactions NBONDS: found 14854 intra-atom interactions NBONDS: found 14888 intra-atom interactions NBONDS: found 14986 intra-atom interactions NBONDS: found 15028 intra-atom interactions NBONDS: found 15074 intra-atom interactions NBONDS: found 15086 intra-atom interactions NBONDS: found 15093 intra-atom interactions NBONDS: found 15120 intra-atom interactions --------------- step= 1400 at 2.80000 ps -------------------------------- | E(kin)+E(total)=26709.432 E(kin)=6067.158 temperature=3006.531 | | Etotal =20642.274 grad(E)=119.317 E(BOND)=2531.028 E(ANGL)=5662.970 | | E(DIHE)=0.000 E(IMPR)=1757.363 E(VDW )=137.154 E(CDIH)=1226.771 | | E(NOE )=8982.241 E(PLAN)=344.747 | ------------------------------------------------------------------------------- NBONDS: found 15129 intra-atom interactions NBONDS: found 15107 intra-atom interactions NBONDS: found 15081 intra-atom interactions NBONDS: found 15079 intra-atom interactions NBONDS: found 15080 intra-atom interactions NBONDS: found 15133 intra-atom interactions NBONDS: found 15192 intra-atom interactions NBONDS: found 15213 intra-atom interactions NBONDS: found 15255 intra-atom interactions NBONDS: found 15292 intra-atom interactions NBONDS: found 15375 intra-atom interactions NBONDS: found 15323 intra-atom interactions --------------- step= 1500 at 3.00000 ps -------------------------------- | E(kin)+E(total)=26733.462 E(kin)=5979.321 temperature=2963.005 | | Etotal =20754.140 grad(E)=122.241 E(BOND)=2712.244 E(ANGL)=5337.068 | | E(DIHE)=0.000 E(IMPR)=1619.619 E(VDW )=142.494 E(CDIH)=1209.821 | | E(NOE )=9366.537 E(PLAN)=366.357 | ------------------------------------------------------------------------------- NBONDS: found 15304 intra-atom interactions NBONDS: found 15341 intra-atom interactions NBONDS: found 15338 intra-atom interactions NBONDS: found 15360 intra-atom interactions NBONDS: found 15354 intra-atom interactions NBONDS: found 15338 intra-atom interactions NBONDS: found 15367 intra-atom interactions NBONDS: found 15376 intra-atom interactions NBONDS: found 15345 intra-atom interactions NBONDS: found 15333 intra-atom interactions NBONDS: found 15317 intra-atom interactions NBONDS: found 15208 intra-atom interactions --------------- step= 1600 at 3.20000 ps -------------------------------- | E(kin)+E(total)=26954.801 E(kin)=6075.344 temperature=3010.588 | | Etotal =20879.456 grad(E)=126.765 E(BOND)=2391.335 E(ANGL)=5740.305 | | E(DIHE)=0.000 E(IMPR)=1748.156 E(VDW )=139.880 E(CDIH)=1302.623 | | E(NOE )=9190.491 E(PLAN)=366.665 | ------------------------------------------------------------------------------- NBONDS: found 15149 intra-atom interactions NBONDS: found 15088 intra-atom interactions NBONDS: found 15059 intra-atom interactions NBONDS: found 15047 intra-atom interactions NBONDS: found 14990 intra-atom interactions NBONDS: found 14938 intra-atom interactions NBONDS: found 14913 intra-atom interactions NBONDS: found 14820 intra-atom interactions NBONDS: found 14722 intra-atom interactions NBONDS: found 14697 intra-atom interactions NBONDS: found 14674 intra-atom interactions --------------- step= 1700 at 3.40000 ps -------------------------------- | E(kin)+E(total)=26893.745 E(kin)=5944.320 temperature=2945.660 | | Etotal =20949.425 grad(E)=130.793 E(BOND)=2579.606 E(ANGL)=5561.552 | | E(DIHE)=0.000 E(IMPR)=2035.421 E(VDW )=128.200 E(CDIH)=1277.588 | | E(NOE )=9008.251 E(PLAN)=358.807 | ------------------------------------------------------------------------------- NBONDS: found 14604 intra-atom interactions NBONDS: found 14609 intra-atom interactions NBONDS: found 14576 intra-atom interactions NBONDS: found 14587 intra-atom interactions NBONDS: found 14610 intra-atom interactions NBONDS: found 14580 intra-atom interactions NBONDS: found 14564 intra-atom interactions NBONDS: found 14533 intra-atom interactions NBONDS: found 14531 intra-atom interactions --------------- step= 1800 at 3.60000 ps -------------------------------- | E(kin)+E(total)=26708.295 E(kin)=6246.291 temperature=3095.299 | | Etotal =20462.004 grad(E)=126.478 E(BOND)=2772.837 E(ANGL)=5393.996 | | E(DIHE)=0.000 E(IMPR)=1953.632 E(VDW )=127.085 E(CDIH)=1219.390 | | E(NOE )=8647.942 E(PLAN)=347.121 | ------------------------------------------------------------------------------- NBONDS: found 14541 intra-atom interactions NBONDS: found 14559 intra-atom interactions NBONDS: found 14531 intra-atom interactions NBONDS: found 14493 intra-atom interactions NBONDS: found 14477 intra-atom interactions NBONDS: found 14440 intra-atom interactions NBONDS: found 14427 intra-atom interactions NBONDS: found 14385 intra-atom interactions NBONDS: found 14278 intra-atom interactions NBONDS: found 14237 intra-atom interactions --------------- step= 1900 at 3.80000 ps -------------------------------- | E(kin)+E(total)=26625.664 E(kin)=6556.301 temperature=3248.923 | | Etotal =20069.363 grad(E)=126.994 E(BOND)=2448.991 E(ANGL)=5163.127 | | E(DIHE)=0.000 E(IMPR)=1854.946 E(VDW )=120.439 E(CDIH)=1219.654 | | E(NOE )=8950.129 E(PLAN)=312.077 | ------------------------------------------------------------------------------- NBONDS: found 14231 intra-atom interactions NBONDS: found 14211 intra-atom interactions NBONDS: found 14208 intra-atom interactions NBONDS: found 14301 intra-atom interactions NBONDS: found 14309 intra-atom interactions NBONDS: found 14353 intra-atom interactions NBONDS: found 14418 intra-atom interactions NBONDS: found 14426 intra-atom interactions NBONDS: found 14473 intra-atom interactions NBONDS: found 14456 intra-atom interactions --------------- step= 2000 at 4.00000 ps -------------------------------- | E(kin)+E(total)=26805.701 E(kin)=5830.296 temperature=2889.156 | | Etotal =20975.405 grad(E)=131.628 E(BOND)=2682.288 E(ANGL)=5554.390 | | E(DIHE)=0.000 E(IMPR)=2004.972 E(VDW )=127.370 E(CDIH)=1065.868 | | E(NOE )=9146.361 E(PLAN)=394.156 | ------------------------------------------------------------------------------- NBONDS: found 14473 intra-atom interactions NBONDS: found 14483 intra-atom interactions NBONDS: found 14439 intra-atom interactions NBONDS: found 14469 intra-atom interactions NBONDS: found 14472 intra-atom interactions NBONDS: found 14507 intra-atom interactions NBONDS: found 14562 intra-atom interactions NBONDS: found 14637 intra-atom interactions NBONDS: found 14691 intra-atom interactions NBONDS: found 14731 intra-atom interactions --------------- step= 2100 at 4.20000 ps -------------------------------- | E(kin)+E(total)=26737.252 E(kin)=6283.184 temperature=3113.581 | | Etotal =20454.068 grad(E)=122.607 E(BOND)=2319.883 E(ANGL)=5655.025 | | E(DIHE)=0.000 E(IMPR)=1905.154 E(VDW )=127.336 E(CDIH)=1092.962 | | E(NOE )=9015.563 E(PLAN)=338.146 | ------------------------------------------------------------------------------- NBONDS: found 14716 intra-atom interactions NBONDS: found 14736 intra-atom interactions NBONDS: found 14754 intra-atom interactions NBONDS: found 14782 intra-atom interactions NBONDS: found 14715 intra-atom interactions NBONDS: found 14669 intra-atom interactions NBONDS: found 14718 intra-atom interactions NBONDS: found 14685 intra-atom interactions NBONDS: found 14639 intra-atom interactions NBONDS: found 14660 intra-atom interactions --------------- step= 2200 at 4.40000 ps -------------------------------- | E(kin)+E(total)=26804.293 E(kin)=5887.536 temperature=2917.521 | | Etotal =20916.757 grad(E)=129.854 E(BOND)=2417.058 E(ANGL)=5471.585 | | E(DIHE)=0.000 E(IMPR)=2232.714 E(VDW )=122.978 E(CDIH)=1221.052 | | E(NOE )=9088.036 E(PLAN)=363.333 | ------------------------------------------------------------------------------- NBONDS: found 14688 intra-atom interactions NBONDS: found 14635 intra-atom interactions NBONDS: found 14616 intra-atom interactions NBONDS: found 14590 intra-atom interactions NBONDS: found 14594 intra-atom interactions NBONDS: found 14566 intra-atom interactions NBONDS: found 14581 intra-atom interactions NBONDS: found 14650 intra-atom interactions NBONDS: found 14721 intra-atom interactions NBONDS: found 14804 intra-atom interactions --------------- step= 2300 at 4.60000 ps -------------------------------- | E(kin)+E(total)=26858.392 E(kin)=6146.937 temperature=3046.065 | | Etotal =20711.455 grad(E)=136.685 E(BOND)=2530.343 E(ANGL)=5268.799 | | E(DIHE)=0.000 E(IMPR)=2203.152 E(VDW )=125.700 E(CDIH)=1166.599 | | E(NOE )=8949.589 E(PLAN)=467.273 | ------------------------------------------------------------------------------- NBONDS: found 14808 intra-atom interactions NBONDS: found 14850 intra-atom interactions NBONDS: found 14881 intra-atom interactions NBONDS: found 14856 intra-atom interactions NBONDS: found 14896 intra-atom interactions NBONDS: found 14957 intra-atom interactions NBONDS: found 15047 intra-atom interactions NBONDS: found 15110 intra-atom interactions NBONDS: found 15126 intra-atom interactions NBONDS: found 15175 intra-atom interactions --------------- step= 2400 at 4.80000 ps -------------------------------- | E(kin)+E(total)=26935.447 E(kin)=6006.731 temperature=2976.588 | | Etotal =20928.716 grad(E)=132.331 E(BOND)=2417.296 E(ANGL)=5798.131 | | E(DIHE)=0.000 E(IMPR)=2166.922 E(VDW )=136.603 E(CDIH)=1234.151 | | E(NOE )=8821.926 E(PLAN)=353.687 | ------------------------------------------------------------------------------- NBONDS: found 15303 intra-atom interactions NBONDS: found 15306 intra-atom interactions NBONDS: found 15373 intra-atom interactions NBONDS: found 15446 intra-atom interactions NBONDS: found 15501 intra-atom interactions NBONDS: found 15507 intra-atom interactions NBONDS: found 15492 intra-atom interactions NBONDS: found 15472 intra-atom interactions NBONDS: found 15416 intra-atom interactions NBONDS: found 15413 intra-atom interactions --------------- step= 2500 at 5.00000 ps -------------------------------- | E(kin)+E(total)=26863.019 E(kin)=6206.075 temperature=3075.371 | | Etotal =20656.945 grad(E)=130.088 E(BOND)=2581.098 E(ANGL)=5895.763 | | E(DIHE)=0.000 E(IMPR)=1876.160 E(VDW )=140.636 E(CDIH)=1246.458 | | E(NOE )=8546.912 E(PLAN)=369.918 | ------------------------------------------------------------------------------- NBONDS: found 15416 intra-atom interactions NBONDS: found 15376 intra-atom interactions NBONDS: found 15393 intra-atom interactions NBONDS: found 15426 intra-atom interactions NBONDS: found 15482 intra-atom interactions NBONDS: found 15472 intra-atom interactions NBONDS: found 15462 intra-atom interactions NBONDS: found 15457 intra-atom interactions NBONDS: found 15487 intra-atom interactions NBONDS: found 15520 intra-atom interactions NBONDS: found 15470 intra-atom interactions --------------- step= 2600 at 5.20000 ps -------------------------------- | E(kin)+E(total)=26860.027 E(kin)=5923.863 temperature=2935.523 | | Etotal =20936.164 grad(E)=129.530 E(BOND)=2696.212 E(ANGL)=5688.091 | | E(DIHE)=0.000 E(IMPR)=2040.633 E(VDW )=142.736 E(CDIH)=1089.227 | | E(NOE )=8908.513 E(PLAN)=370.752 | ------------------------------------------------------------------------------- NBONDS: found 15440 intra-atom interactions NBONDS: found 15383 intra-atom interactions NBONDS: found 15343 intra-atom interactions NBONDS: found 15328 intra-atom interactions NBONDS: found 15292 intra-atom interactions NBONDS: found 15277 intra-atom interactions NBONDS: found 15221 intra-atom interactions NBONDS: found 15200 intra-atom interactions NBONDS: found 15224 intra-atom interactions --------------- step= 2700 at 5.40000 ps -------------------------------- | E(kin)+E(total)=26788.067 E(kin)=5962.865 temperature=2954.850 | | Etotal =20825.202 grad(E)=133.100 E(BOND)=2694.245 E(ANGL)=5600.305 | | E(DIHE)=0.000 E(IMPR)=1909.558 E(VDW )=137.130 E(CDIH)=1204.230 | | E(NOE )=8942.510 E(PLAN)=337.225 | ------------------------------------------------------------------------------- NBONDS: found 15236 intra-atom interactions NBONDS: found 15231 intra-atom interactions NBONDS: found 15238 intra-atom interactions NBONDS: found 15258 intra-atom interactions NBONDS: found 15247 intra-atom interactions NBONDS: found 15212 intra-atom interactions NBONDS: found 15192 intra-atom interactions NBONDS: found 15208 intra-atom interactions NBONDS: found 15303 intra-atom interactions --------------- step= 2800 at 5.60000 ps -------------------------------- | E(kin)+E(total)=26844.586 E(kin)=6022.091 temperature=2984.199 | | Etotal =20822.495 grad(E)=131.908 E(BOND)=2671.766 E(ANGL)=5705.378 | | E(DIHE)=0.000 E(IMPR)=1919.911 E(VDW )=141.950 E(CDIH)=1173.281 | | E(NOE )=8818.834 E(PLAN)=391.376 | ------------------------------------------------------------------------------- NBONDS: found 15349 intra-atom interactions NBONDS: found 15417 intra-atom interactions NBONDS: found 15502 intra-atom interactions NBONDS: found 15572 intra-atom interactions NBONDS: found 15564 intra-atom interactions NBONDS: found 15623 intra-atom interactions NBONDS: found 15705 intra-atom interactions NBONDS: found 15767 intra-atom interactions NBONDS: found 15799 intra-atom interactions NBONDS: found 15862 intra-atom interactions --------------- step= 2900 at 5.80000 ps -------------------------------- | E(kin)+E(total)=26677.843 E(kin)=6088.809 temperature=3017.261 | | Etotal =20589.034 grad(E)=133.153 E(BOND)=2498.956 E(ANGL)=5567.509 | | E(DIHE)=0.000 E(IMPR)=2102.716 E(VDW )=148.214 E(CDIH)=1117.167 | | E(NOE )=8839.577 E(PLAN)=314.894 | ------------------------------------------------------------------------------- NBONDS: found 15966 intra-atom interactions NBONDS: found 16030 intra-atom interactions NBONDS: found 16074 intra-atom interactions NBONDS: found 16119 intra-atom interactions NBONDS: found 16096 intra-atom interactions NBONDS: found 16133 intra-atom interactions NBONDS: found 16130 intra-atom interactions NBONDS: found 16078 intra-atom interactions NBONDS: found 16057 intra-atom interactions --------------- step= 3000 at 6.00000 ps -------------------------------- | E(kin)+E(total)=26747.008 E(kin)=6002.732 temperature=2974.606 | | Etotal =20744.276 grad(E)=133.850 E(BOND)=2708.379 E(ANGL)=5511.189 | | E(DIHE)=0.000 E(IMPR)=1981.784 E(VDW )=149.880 E(CDIH)=1144.475 | | E(NOE )=8813.670 E(PLAN)=434.899 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 0.00000 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] : 0.00000 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] : 0.00000 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 16055 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=42049.035 E(kin)=6002.732 temperature=2974.606 | | Etotal =36046.304 grad(E)=330.452 E(BOND)=6770.948 E(ANGL)=13777.972 | | E(DIHE)=0.000 E(IMPR)=4954.460 E(VDW )=149.880 E(CDIH)=1144.475 | | E(NOE )=8813.670 E(PLAN)=434.899 | ------------------------------------------------------------------------------- NBONDS: found 16122 intra-atom interactions NBONDS: found 16170 intra-atom interactions NBONDS: found 16220 intra-atom interactions NBONDS: found 16294 intra-atom interactions NBONDS: found 16312 intra-atom interactions NBONDS: found 16346 intra-atom interactions NBONDS: found 16389 intra-atom interactions NBONDS: found 16326 intra-atom interactions NBONDS: found 16394 intra-atom interactions NBONDS: found 16403 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=34340.542 E(kin)=6588.872 temperature=3265.063 | | Etotal =27751.670 grad(E)=217.909 E(BOND)=2836.125 E(ANGL)=8391.930 | | E(DIHE)=0.000 E(IMPR)=2355.764 E(VDW )=154.851 E(CDIH)=1182.276 | | E(NOE )=12369.648 E(PLAN)=461.075 | ------------------------------------------------------------------------------- NBONDS: found 16349 intra-atom interactions NBONDS: found 16395 intra-atom interactions NBONDS: found 16462 intra-atom interactions NBONDS: found 16555 intra-atom interactions NBONDS: found 16565 intra-atom interactions NBONDS: found 16542 intra-atom interactions NBONDS: found 16592 intra-atom interactions NBONDS: found 16657 intra-atom interactions NBONDS: found 16628 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=33237.155 E(kin)=6079.765 temperature=3012.779 | | Etotal =27157.390 grad(E)=215.287 E(BOND)=2658.736 E(ANGL)=8124.259 | | E(DIHE)=0.000 E(IMPR)=2267.933 E(VDW )=161.709 E(CDIH)=1210.173 | | E(NOE )=12333.575 E(PLAN)=401.004 | ------------------------------------------------------------------------------- NBONDS: found 16639 intra-atom interactions NBONDS: found 16704 intra-atom interactions NBONDS: found 16719 intra-atom interactions NBONDS: found 16770 intra-atom interactions NBONDS: found 16802 intra-atom interactions NBONDS: found 16923 intra-atom interactions NBONDS: found 16942 intra-atom interactions NBONDS: found 16988 intra-atom interactions NBONDS: found 16976 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=33058.377 E(kin)=6150.428 temperature=3047.795 | | Etotal =26907.950 grad(E)=200.421 E(BOND)=2784.538 E(ANGL)=7898.022 | | E(DIHE)=0.000 E(IMPR)=2078.941 E(VDW )=165.427 E(CDIH)=1170.495 | | E(NOE )=12384.533 E(PLAN)=425.993 | ------------------------------------------------------------------------------- NBONDS: found 16965 intra-atom interactions NBONDS: found 17034 intra-atom interactions NBONDS: found 16989 intra-atom interactions NBONDS: found 16985 intra-atom interactions NBONDS: found 16988 intra-atom interactions NBONDS: found 16944 intra-atom interactions NBONDS: found 16997 intra-atom interactions NBONDS: found 17001 intra-atom interactions NBONDS: found 17051 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=32962.559 E(kin)=6103.009 temperature=3024.297 | | Etotal =26859.550 grad(E)=197.136 E(BOND)=3074.869 E(ANGL)=7291.363 | | E(DIHE)=0.000 E(IMPR)=2122.925 E(VDW )=173.112 E(CDIH)=1105.827 | | E(NOE )=12663.646 E(PLAN)=427.808 | ------------------------------------------------------------------------------- NBONDS: found 17069 intra-atom interactions NBONDS: found 17148 intra-atom interactions NBONDS: found 17213 intra-atom interactions NBONDS: found 17334 intra-atom interactions NBONDS: found 17446 intra-atom interactions NBONDS: found 17553 intra-atom interactions NBONDS: found 17657 intra-atom interactions NBONDS: found 17740 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=32987.930 E(kin)=6006.512 temperature=2976.479 | | Etotal =26981.417 grad(E)=205.316 E(BOND)=2750.450 E(ANGL)=7406.261 | | E(DIHE)=0.000 E(IMPR)=2135.331 E(VDW )=178.976 E(CDIH)=1146.746 | | E(NOE )=12925.232 E(PLAN)=438.421 | ------------------------------------------------------------------------------- NBONDS: found 17738 intra-atom interactions NBONDS: found 17818 intra-atom interactions NBONDS: found 17893 intra-atom interactions NBONDS: found 18003 intra-atom interactions NBONDS: found 18058 intra-atom interactions NBONDS: found 18115 intra-atom interactions NBONDS: found 18056 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=33073.446 E(kin)=5823.735 temperature=2885.905 | | Etotal =27249.710 grad(E)=206.055 E(BOND)=2698.506 E(ANGL)=7952.477 | | E(DIHE)=0.000 E(IMPR)=2034.131 E(VDW )=191.476 E(CDIH)=1163.979 | | E(NOE )=12775.127 E(PLAN)=434.016 | ------------------------------------------------------------------------------- NBONDS: found 18163 intra-atom interactions NBONDS: found 18313 intra-atom interactions NBONDS: found 18272 intra-atom interactions NBONDS: found 18227 intra-atom interactions NBONDS: found 18310 intra-atom interactions NBONDS: found 18332 intra-atom interactions NBONDS: found 18330 intra-atom interactions NBONDS: found 18269 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=33022.604 E(kin)=6428.909 temperature=3185.795 | | Etotal =26593.695 grad(E)=196.420 E(BOND)=2444.993 E(ANGL)=7689.179 | | E(DIHE)=0.000 E(IMPR)=2274.949 E(VDW )=188.245 E(CDIH)=1142.119 | | E(NOE )=12454.092 E(PLAN)=400.118 | ------------------------------------------------------------------------------- NBONDS: found 18201 intra-atom interactions NBONDS: found 18132 intra-atom interactions NBONDS: found 18155 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00000 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 18:25:48 created by user: COOR>ATOM 1 P GUA 1 12.148 5.107 8.580 1.00 0.00 A COOR>ATOM 2 O1P GUA 1 12.456 4.522 8.142 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 = 2.7079 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6020 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0426 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8263 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1877 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8734 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2337 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.1342 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6207 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.0811 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.6706 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.0246 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.4888 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.1696 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6490 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9670 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.5591 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8439 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.5573 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9370 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6032 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 15517 intra-atom interactions NBONDS: found 15583 intra-atom interactions NBONDS: found 15633 intra-atom interactions NBONDS: found 15686 intra-atom interactions NBONDS: found 15766 intra-atom interactions NBONDS: found 15838 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0002 ----------------------- | Etotal =108479.286 grad(E)=365.830 E(BOND)=16708.878 E(VDW )=11929.708 | | E(CDIH)=4366.166 E(NOE )=74882.089 E(PLAN)=592.445 | ------------------------------------------------------------------------------- NBONDS: found 15882 intra-atom interactions NBONDS: found 15910 intra-atom interactions NBONDS: found 15863 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0002 ----------------------- | Etotal =60753.605 grad(E)=156.508 E(BOND)=4437.779 E(VDW )=8431.828 | | E(CDIH)=3470.123 E(NOE )=44012.888 E(PLAN)=400.988 | ------------------------------------------------------------------------------- NBONDS: found 15851 intra-atom interactions NBONDS: found 15816 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =42436.236 grad(E)=111.070 E(BOND)=2136.867 E(VDW )=6533.864 | | E(CDIH)=2709.629 E(NOE )=30767.629 E(PLAN)=288.247 | ------------------------------------------------------------------------------- NBONDS: found 15801 intra-atom interactions NBONDS: found 15720 intra-atom interactions NBONDS: found 15659 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0002 ----------------------- | Etotal =33456.451 grad(E)=112.283 E(BOND)=1854.218 E(VDW )=5302.151 | | E(CDIH)=2254.564 E(NOE )=23761.521 E(PLAN)=283.997 | ------------------------------------------------------------------------------- NBONDS: found 15588 intra-atom interactions NBONDS: found 15483 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =26286.136 grad(E)=95.096 E(BOND)=1199.615 E(VDW )=4238.316 | | E(CDIH)=2113.379 E(NOE )=18445.241 E(PLAN)=289.585 | ------------------------------------------------------------------------------- NBONDS: found 15423 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =21573.599 grad(E)=52.846 E(BOND)=718.141 E(VDW )=3216.969 | | E(CDIH)=1664.095 E(NOE )=15664.800 E(PLAN)=309.595 | ------------------------------------------------------------------------------- NBONDS: found 15307 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0002 ----------------------- | Etotal =19090.551 grad(E)=54.896 E(BOND)=684.969 E(VDW )=2590.851 | | E(CDIH)=1515.593 E(NOE )=14021.934 E(PLAN)=277.205 | ------------------------------------------------------------------------------- NBONDS: found 15194 intra-atom interactions NBONDS: found 15069 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =17312.230 grad(E)=53.679 E(BOND)=660.384 E(VDW )=2490.104 | | E(CDIH)=1422.269 E(NOE )=12469.157 E(PLAN)=270.316 | ------------------------------------------------------------------------------- NBONDS: found 14974 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =15452.102 grad(E)=48.245 E(BOND)=593.081 E(VDW )=2267.946 | | E(CDIH)=1354.435 E(NOE )=10985.619 E(PLAN)=251.023 | ------------------------------------------------------------------------------- NBONDS: found 14880 intra-atom interactions NBONDS: found 14584 intra-atom interactions NBONDS: found 14813 intra-atom interactions NBONDS: found 14503 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0009 ----------------------- | Etotal =45251.775 grad(E)=520.918 E(BOND)=27953.576 E(VDW )=2841.273 | | E(CDIH)=2421.742 E(NOE )=11809.286 E(PLAN)=225.898 | ------------------------------------------------------------------------------- NBONDS: found 14778 intra-atom interactions NBONDS: found 14526 intra-atom interactions NBONDS: found 14741 intra-atom interactions NBONDS: found 14609 intra-atom interactions NBONDS: found 14738 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0000 ----------------------- | Etotal =13206.683 grad(E)=45.311 E(BOND)=454.720 E(VDW )=1711.052 | | E(CDIH)=1403.861 E(NOE )=9420.719 E(PLAN)=216.331 | ------------------------------------------------------------------------------- --------------- cycle= 120 ------ stepsize= 0.0000 ----------------------- | Etotal =12588.298 grad(E)=25.218 E(BOND)=302.047 E(VDW )=1614.054 | | E(CDIH)=1309.579 E(NOE )=9150.720 E(PLAN)=211.898 | ------------------------------------------------------------------------------- --------------- cycle= 130 ------ stepsize= 0.0000 ----------------------- | Etotal =12587.707 grad(E)=25.277 E(BOND)=302.151 E(VDW )=1613.889 | | E(CDIH)=1309.457 E(NOE )=9150.322 E(PLAN)=211.887 | ------------------------------------------------------------------------------- --------------- cycle= 140 ------ stepsize= 0.0000 ----------------------- | Etotal =12587.701 grad(E)=25.278 E(BOND)=302.152 E(VDW )=1613.888 | | E(CDIH)=1309.456 E(NOE )=9150.318 E(PLAN)=211.887 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =12587.701 grad(E)=25.278 E(BOND)=302.152 E(VDW )=1613.888 | | E(CDIH)=1309.456 E(NOE )=9150.318 E(PLAN)=211.887 | ------------------------------------------------------------------------------- %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 14648 intra-atom interactions NBONDS: found 14573 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =96179.026 grad(E)=351.716 E(BOND)=12211.325 E(ANGL)=64936.884 | | E(VDW )=3267.274 E(CDIH)=2652.474 E(NOE )=12727.031 E(PLAN)=384.039 | ------------------------------------------------------------------------------- NBONDS: found 14541 intra-atom interactions NBONDS: found 14525 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =66104.773 grad(E)=162.467 E(BOND)=4189.574 E(ANGL)=37573.270 | | E(VDW )=4132.077 E(CDIH)=3043.512 E(NOE )=16748.770 E(PLAN)=417.570 | ------------------------------------------------------------------------------- NBONDS: found 14467 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =55795.175 grad(E)=94.776 E(BOND)=2607.369 E(ANGL)=28751.138 | | E(VDW )=4257.034 E(CDIH)=3057.988 E(NOE )=16701.466 E(PLAN)=420.181 | ------------------------------------------------------------------------------- NBONDS: found 14359 intra-atom interactions NBONDS: found 14296 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =49989.554 grad(E)=108.604 E(BOND)=2657.769 E(ANGL)=22441.145 | | E(VDW )=4250.414 E(CDIH)=3068.903 E(NOE )=17133.763 E(PLAN)=437.559 | ------------------------------------------------------------------------------- NBONDS: found 14240 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =45397.950 grad(E)=71.425 E(BOND)=1976.204 E(ANGL)=19702.214 | | E(VDW )=3957.571 E(CDIH)=3145.337 E(NOE )=16185.712 E(PLAN)=430.913 | ------------------------------------------------------------------------------- NBONDS: found 14152 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =42829.941 grad(E)=68.024 E(BOND)=1886.272 E(ANGL)=17790.639 | | E(VDW )=3702.837 E(CDIH)=3366.780 E(NOE )=15646.455 E(PLAN)=436.957 | ------------------------------------------------------------------------------- NBONDS: found 14051 intra-atom interactions NBONDS: found 13964 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =40072.731 grad(E)=61.447 E(BOND)=1875.018 E(ANGL)=15855.441 | | E(VDW )=3458.844 E(CDIH)=3483.859 E(NOE )=14962.223 E(PLAN)=437.345 | ------------------------------------------------------------------------------- NBONDS: found 13919 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =38040.585 grad(E)=54.298 E(BOND)=1680.926 E(ANGL)=14608.888 | | E(VDW )=3271.061 E(CDIH)=3462.792 E(NOE )=14576.738 E(PLAN)=440.180 | ------------------------------------------------------------------------------- NBONDS: found 13857 intra-atom interactions NBONDS: found 13813 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =36207.794 grad(E)=49.784 E(BOND)=1569.793 E(ANGL)=13819.192 | | E(VDW )=2988.974 E(CDIH)=3383.110 E(NOE )=14012.921 E(PLAN)=433.804 | ------------------------------------------------------------------------------- NBONDS: found 13772 intra-atom interactions NBONDS: found 13677 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =34853.473 grad(E)=41.197 E(BOND)=1451.347 E(ANGL)=13129.367 | | E(VDW )=2719.824 E(CDIH)=3282.398 E(NOE )=13851.163 E(PLAN)=419.374 | ------------------------------------------------------------------------------- NBONDS: found 13626 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0001 ----------------------- | Etotal =33896.481 grad(E)=32.416 E(BOND)=1309.399 E(ANGL)=12772.493 | | E(VDW )=2637.647 E(CDIH)=3209.279 E(NOE )=13561.651 E(PLAN)=406.011 | ------------------------------------------------------------------------------- NBONDS: found 13549 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0001 ----------------------- | Etotal =33175.648 grad(E)=36.219 E(BOND)=1341.275 E(ANGL)=12321.241 | | E(VDW )=2645.868 E(CDIH)=3126.262 E(NOE )=13342.455 E(PLAN)=398.546 | ------------------------------------------------------------------------------- NBONDS: found 13502 intra-atom interactions NBONDS: found 13437 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0001 ----------------------- | Etotal =31823.781 grad(E)=48.989 E(BOND)=1261.311 E(ANGL)=11625.963 | | E(VDW )=2482.922 E(CDIH)=2924.823 E(NOE )=13145.101 E(PLAN)=383.661 | ------------------------------------------------------------------------------- NBONDS: found 13309 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0001 ----------------------- | Etotal =30239.738 grad(E)=46.508 E(BOND)=1331.446 E(ANGL)=10819.582 | | E(VDW )=2151.511 E(CDIH)=2805.192 E(NOE )=12778.883 E(PLAN)=353.124 | ------------------------------------------------------------------------------- NBONDS: found 13212 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =29038.563 grad(E)=41.362 E(BOND)=1202.491 E(ANGL)=10264.203 | | E(VDW )=1938.808 E(CDIH)=2742.740 E(NOE )=12551.139 E(PLAN)=339.181 | ------------------------------------------------------------------------------- NBONDS: found 13155 intra-atom interactions --------------- cycle= 160 ------ stepsize= 0.0001 ----------------------- | Etotal =28210.063 grad(E)=34.762 E(BOND)=1148.787 E(ANGL)=9871.935 | | E(VDW )=1745.592 E(CDIH)=2699.428 E(NOE )=12412.207 E(PLAN)=332.114 | ------------------------------------------------------------------------------- --------------- cycle= 170 ------ stepsize= 0.0001 ----------------------- | Etotal =27449.412 grad(E)=36.177 E(BOND)=1138.197 E(ANGL)=9522.033 | | E(VDW )=1568.937 E(CDIH)=2700.086 E(NOE )=12200.001 E(PLAN)=320.157 | ------------------------------------------------------------------------------- NBONDS: found 13104 intra-atom interactions NBONDS: found 13055 intra-atom interactions --------------- cycle= 180 ------ stepsize= 0.0001 ----------------------- | Etotal =26613.842 grad(E)=42.889 E(BOND)=1180.162 E(ANGL)=9102.706 | | E(VDW )=1496.697 E(CDIH)=2722.477 E(NOE )=11800.120 E(PLAN)=311.680 | ------------------------------------------------------------------------------- --------------- cycle= 190 ------ stepsize= 0.0001 ----------------------- | Etotal =25884.883 grad(E)=34.950 E(BOND)=1033.808 E(ANGL)=9055.339 | | E(VDW )=1449.086 E(CDIH)=2636.498 E(NOE )=11394.572 E(PLAN)=315.580 | ------------------------------------------------------------------------------- NBONDS: found 12986 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =25229.505 grad(E)=36.452 E(BOND)=1005.779 E(ANGL)=8869.485 | | E(VDW )=1343.810 E(CDIH)=2624.398 E(NOE )=11080.561 E(PLAN)=305.471 | ------------------------------------------------------------------------------- NBONDS: found 12926 intra-atom interactions --------------- cycle= 210 ------ stepsize= 0.0001 ----------------------- | Etotal =24670.559 grad(E)=28.112 E(BOND)=998.778 E(ANGL)=8723.371 | | E(VDW )=1367.981 E(CDIH)=2616.433 E(NOE )=10673.295 E(PLAN)=290.701 | ------------------------------------------------------------------------------- NBONDS: found 12849 intra-atom interactions --------------- cycle= 220 ------ stepsize= 0.0001 ----------------------- | Etotal =24258.228 grad(E)=22.779 E(BOND)=915.569 E(ANGL)=8646.225 | | E(VDW )=1381.687 E(CDIH)=2617.541 E(NOE )=10419.924 E(PLAN)=277.282 | ------------------------------------------------------------------------------- NBONDS: found 12843 intra-atom interactions NBONDS: found 12831 intra-atom interactions --------------- cycle= 230 ------ stepsize= 0.0001 ----------------------- | Etotal =23848.766 grad(E)=26.587 E(BOND)=878.980 E(ANGL)=8598.766 | | E(VDW )=1379.265 E(CDIH)=2613.713 E(NOE )=10111.856 E(PLAN)=266.186 | ------------------------------------------------------------------------------- --------------- cycle= 240 ------ stepsize= 0.0001 ----------------------- | Etotal =23395.724 grad(E)=26.407 E(BOND)=848.387 E(ANGL)=8416.975 | | E(VDW )=1339.286 E(CDIH)=2614.004 E(NOE )=9903.015 E(PLAN)=274.058 | ------------------------------------------------------------------------------- NBONDS: found 12823 intra-atom interactions --------------- cycle= 250 ------ stepsize= 0.0001 ----------------------- | Etotal =23014.066 grad(E)=24.293 E(BOND)=835.741 E(ANGL)=8305.966 | | E(VDW )=1357.334 E(CDIH)=2607.932 E(NOE )=9632.779 E(PLAN)=274.314 | ------------------------------------------------------------------------------- NBONDS: found 12765 intra-atom interactions --------------- cycle= 260 ------ stepsize= 0.0001 ----------------------- | Etotal =22652.225 grad(E)=21.954 E(BOND)=825.679 E(ANGL)=8178.016 | | E(VDW )=1346.303 E(CDIH)=2590.012 E(NOE )=9439.715 E(PLAN)=272.500 | ------------------------------------------------------------------------------- --------------- cycle= 270 ------ stepsize= 0.0001 ----------------------- | Etotal =22317.429 grad(E)=21.716 E(BOND)=831.924 E(ANGL)=8118.302 | | E(VDW )=1282.164 E(CDIH)=2553.824 E(NOE )=9264.427 E(PLAN)=266.788 | ------------------------------------------------------------------------------- NBONDS: found 12685 intra-atom interactions --------------- cycle= 280 ------ stepsize= 0.0001 ----------------------- | Etotal =21988.048 grad(E)=22.789 E(BOND)=810.735 E(ANGL)=8063.348 | | E(VDW )=1226.381 E(CDIH)=2512.095 E(NOE )=9112.248 E(PLAN)=263.240 | ------------------------------------------------------------------------------- NBONDS: found 12603 intra-atom interactions --------------- cycle= 290 ------ stepsize= 0.0001 ----------------------- | Etotal =21672.418 grad(E)=26.939 E(BOND)=803.577 E(ANGL)=8048.578 | | E(VDW )=1198.995 E(CDIH)=2455.273 E(NOE )=8892.904 E(PLAN)=273.091 | ------------------------------------------------------------------------------- NBONDS: found 12473 intra-atom interactions --------------- cycle= 300 ------ stepsize= 0.0001 ----------------------- | Etotal =21365.948 grad(E)=24.328 E(BOND)=807.416 E(ANGL)=8020.627 | | E(VDW )=1151.878 E(CDIH)=2413.084 E(NOE )=8688.176 E(PLAN)=284.768 | ------------------------------------------------------------------------------- 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= 0.145943816E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 0.00000 0.00001 0.00001 velocity [A/ps] : -0.33229 0.08728 -0.04863 ang. mom. [amu A/ps] : 73786.52985 110089.16424 139421.02315 kin. ener. [Kcal/mol] : 9.74053 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00000 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 12440 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=26897.896 E(kin)=6243.927 temperature=3094.128 | | Etotal =20653.969 grad(E)=69.186 E(BOND)=80.742 E(ANGL)=802.063 | | E(DIHE)=0.000 E(IMPR)=7233.260 E(VDW )=1151.878 E(CDIH)=2413.084 | | E(NOE )=8688.176 E(PLAN)=284.768 | ------------------------------------------------------------------------------- NBONDS: found 12437 intra-atom interactions NBONDS: found 12400 intra-atom interactions NBONDS: found 12330 intra-atom interactions NBONDS: found 12263 intra-atom interactions NBONDS: found 12196 intra-atom interactions NBONDS: found 12066 intra-atom interactions NBONDS: found 11955 intra-atom interactions NBONDS: found 11916 intra-atom interactions NBONDS: found 11869 intra-atom interactions NBONDS: found 11850 intra-atom interactions NBONDS: found 11776 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=25341.213 E(kin)=7015.755 temperature=3476.601 | | Etotal =18325.458 grad(E)=67.081 E(BOND)=2469.610 E(ANGL)=5044.698 | | E(DIHE)=0.000 E(IMPR)=3874.455 E(VDW )=496.401 E(CDIH)=1394.249 | | E(NOE )=4810.297 E(PLAN)=235.749 | ------------------------------------------------------------------------------- NBONDS: found 11702 intra-atom interactions NBONDS: found 11662 intra-atom interactions NBONDS: found 11584 intra-atom interactions NBONDS: found 11499 intra-atom interactions NBONDS: found 11396 intra-atom interactions NBONDS: found 11347 intra-atom interactions NBONDS: found 11288 intra-atom interactions NBONDS: found 11197 intra-atom interactions NBONDS: found 11129 intra-atom interactions NBONDS: found 11060 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=21905.148 E(kin)=6900.180 temperature=3419.329 | | Etotal =15004.968 grad(E)=64.992 E(BOND)=2166.660 E(ANGL)=4203.839 | | E(DIHE)=0.000 E(IMPR)=2962.730 E(VDW )=339.891 E(CDIH)=1195.268 | | E(NOE )=3903.137 E(PLAN)=233.443 | ------------------------------------------------------------------------------- NBONDS: found 11010 intra-atom interactions NBONDS: found 10960 intra-atom interactions NBONDS: found 10898 intra-atom interactions NBONDS: found 10806 intra-atom interactions NBONDS: found 10741 intra-atom interactions NBONDS: found 10680 intra-atom interactions NBONDS: found 10645 intra-atom interactions NBONDS: found 10596 intra-atom interactions NBONDS: found 10563 intra-atom interactions NBONDS: found 10532 intra-atom interactions NBONDS: found 10452 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=19245.591 E(kin)=6501.349 temperature=3221.692 | | Etotal =12744.241 grad(E)=61.648 E(BOND)=1979.835 E(ANGL)=3813.410 | | E(DIHE)=0.000 E(IMPR)=2461.409 E(VDW )=228.427 E(CDIH)=710.671 | | E(NOE )=3440.221 E(PLAN)=110.268 | ------------------------------------------------------------------------------- NBONDS: found 10429 intra-atom interactions NBONDS: found 10419 intra-atom interactions NBONDS: found 10436 intra-atom interactions NBONDS: found 10423 intra-atom interactions NBONDS: found 10459 intra-atom interactions NBONDS: found 10507 intra-atom interactions NBONDS: found 10512 intra-atom interactions NBONDS: found 10545 intra-atom interactions NBONDS: found 10514 intra-atom interactions NBONDS: found 10526 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=17802.254 E(kin)=6228.835 temperature=3086.649 | | Etotal =11573.419 grad(E)=57.712 E(BOND)=1837.852 E(ANGL)=3354.911 | | E(DIHE)=0.000 E(IMPR)=2266.963 E(VDW )=196.095 E(CDIH)=686.979 | | E(NOE )=3123.937 E(PLAN)=106.681 | ------------------------------------------------------------------------------- NBONDS: found 10571 intra-atom interactions NBONDS: found 10576 intra-atom interactions NBONDS: found 10588 intra-atom interactions NBONDS: found 10592 intra-atom interactions NBONDS: found 10594 intra-atom interactions NBONDS: found 10596 intra-atom interactions NBONDS: found 10552 intra-atom interactions NBONDS: found 10538 intra-atom interactions NBONDS: found 10493 intra-atom interactions NBONDS: found 10511 intra-atom interactions NBONDS: found 10527 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=17266.160 E(kin)=6036.964 temperature=2991.569 | | Etotal =11229.196 grad(E)=61.155 E(BOND)=2039.012 E(ANGL)=3263.963 | | E(DIHE)=0.000 E(IMPR)=2060.277 E(VDW )=86.591 E(CDIH)=429.367 | | E(NOE )=3239.283 E(PLAN)=110.704 | ------------------------------------------------------------------------------- NBONDS: found 10525 intra-atom interactions NBONDS: found 10520 intra-atom interactions NBONDS: found 10471 intra-atom interactions NBONDS: found 10494 intra-atom interactions NBONDS: found 10512 intra-atom interactions NBONDS: found 10530 intra-atom interactions NBONDS: found 10523 intra-atom interactions NBONDS: found 10509 intra-atom interactions NBONDS: found 10503 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=1730