X-PLOR: V3.840 user: on: Alpha/OSF at: 16-Aug-96 19:23:01 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=15261.9483032227 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 19:21:24 created by user: COOR>ATOM 1 P GUA 1 14.209 3.014 7.103 1.00 0.00 A COOR>ATOM 2 O1P GUA 1 11.537 5.626 8.265 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 = 2.5664 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.5761 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0485 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2279 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1886 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.5332 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6533 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.4059 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6780 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.4111 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.6899 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.6002 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.7072 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.2357 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1937 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.5336 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.7696 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0891 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.7903 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2004 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6896 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 14892 intra-atom interactions NBONDS: found 14953 intra-atom interactions NBONDS: found 15103 intra-atom interactions NBONDS: found 15232 intra-atom interactions NBONDS: found 15398 intra-atom interactions NBONDS: found 15622 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =125236.167 grad(E)=384.715 E(BOND)=20523.948 E(VDW )=11569.985 | | E(CDIH)=5156.658 E(NOE )=87277.763 E(PLAN)=707.814 | ------------------------------------------------------------------------------- NBONDS: found 15716 intra-atom interactions NBONDS: found 15823 intra-atom interactions NBONDS: found 15927 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =68398.206 grad(E)=152.254 E(BOND)=3574.781 E(VDW )=9576.851 | | E(CDIH)=3632.338 E(NOE )=51065.955 E(PLAN)=548.281 | ------------------------------------------------------------------------------- NBONDS: found 15926 intra-atom interactions NBONDS: found 15917 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0002 ----------------------- | Etotal =50702.425 grad(E)=123.936 E(BOND)=2381.052 E(VDW )=7179.780 | | E(CDIH)=3134.021 E(NOE )=37617.868 E(PLAN)=389.704 | ------------------------------------------------------------------------------- NBONDS: found 15895 intra-atom interactions NBONDS: found 15861 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0002 ----------------------- | Etotal =39175.658 grad(E)=93.295 E(BOND)=1850.914 E(VDW )=5392.214 | | E(CDIH)=2908.011 E(NOE )=28696.953 E(PLAN)=327.565 | ------------------------------------------------------------------------------- NBONDS: found 15901 intra-atom interactions NBONDS: found 15800 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =31863.659 grad(E)=89.102 E(BOND)=1502.816 E(VDW )=4292.422 | | E(CDIH)=2568.088 E(NOE )=23171.440 E(PLAN)=328.893 | ------------------------------------------------------------------------------- NBONDS: found 15758 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =26450.423 grad(E)=61.521 E(BOND)=978.150 E(VDW )=3462.180 | | E(CDIH)=1935.119 E(NOE )=19742.619 E(PLAN)=332.354 | ------------------------------------------------------------------------------- NBONDS: found 15703 intra-atom interactions NBONDS: found 15620 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =22570.890 grad(E)=52.143 E(BOND)=714.891 E(VDW )=2399.909 | | E(CDIH)=1781.924 E(NOE )=17327.627 E(PLAN)=346.539 | ------------------------------------------------------------------------------- NBONDS: found 15589 intra-atom interactions NBONDS: found 15375 intra-atom interactions NBONDS: found 15573 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =20520.060 grad(E)=43.911 E(BOND)=640.768 E(VDW )=1994.082 | | E(CDIH)=1797.822 E(NOE )=15750.484 E(PLAN)=336.904 | ------------------------------------------------------------------------------- --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =19087.479 grad(E)=52.172 E(BOND)=610.740 E(VDW )=1744.757 | | E(CDIH)=1526.242 E(NOE )=14892.377 E(PLAN)=313.364 | ------------------------------------------------------------------------------- NBONDS: found 15568 intra-atom interactions NBONDS: found 15346 intra-atom interactions NBONDS: found 15518 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0002 ----------------------- | Etotal =17990.859 grad(E)=52.296 E(BOND)=552.005 E(VDW )=1515.208 | | E(CDIH)=1517.059 E(NOE )=14115.072 E(PLAN)=291.515 | ------------------------------------------------------------------------------- NBONDS: found 15419 intra-atom interactions NBONDS: found 15154 intra-atom interactions NBONDS: found 15378 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0000 ----------------------- | Etotal =16863.575 grad(E)=45.261 E(BOND)=524.020 E(VDW )=1233.494 | | E(CDIH)=1617.377 E(NOE )=13203.542 E(PLAN)=285.142 | ------------------------------------------------------------------------------- NBONDS: found 15159 intra-atom interactions NBONDS: found 15334 intra-atom interactions NBONDS: found 15224 intra-atom interactions NBONDS: found 15316 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0001 ----------------------- | Etotal =15571.385 grad(E)=33.257 E(BOND)=388.039 E(VDW )=1100.738 | | E(CDIH)=1606.360 E(NOE )=12203.113 E(PLAN)=273.134 | ------------------------------------------------------------------------------- NBONDS: found 15275 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0002 ----------------------- | Etotal =14251.901 grad(E)=34.061 E(BOND)=311.050 E(VDW )=975.823 | | E(CDIH)=1179.920 E(NOE )=11520.766 E(PLAN)=264.342 | ------------------------------------------------------------------------------- --------------- cycle= 140 ------ stepsize= 0.0000 ----------------------- | Etotal =14192.191 grad(E)=27.126 E(BOND)=283.221 E(VDW )=971.171 | | E(CDIH)=1175.666 E(NOE )=11498.226 E(PLAN)=263.907 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =14189.176 grad(E)=26.877 E(BOND)=282.357 E(VDW )=970.897 | | E(CDIH)=1175.350 E(NOE )=11496.694 E(PLAN)=263.878 | ------------------------------------------------------------------------------- --------------- cycle= 160 ------ stepsize= 0.0000 ----------------------- | Etotal =14189.164 grad(E)=26.876 E(BOND)=282.353 E(VDW )=970.896 | | E(CDIH)=1175.348 E(NOE )=11496.688 E(PLAN)=263.878 | ------------------------------------------------------------------------------- --------------- cycle= 170 ------ stepsize= 0.0000 ----------------------- | Etotal =14411.844 grad(E)=27.686 E(BOND)=282.353 E(VDW )=970.896 | | E(CDIH)=1398.029 E(NOE )=11496.688 E(PLAN)=263.878 | ------------------------------------------------------------------------------- %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 15230 intra-atom interactions NBONDS: found 15168 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =117667.633 grad(E)=405.213 E(BOND)=12823.178 E(ANGL)=81471.016 | | E(VDW )=3737.834 E(CDIH)=2995.827 E(NOE )=16157.588 E(PLAN)=482.191 | ------------------------------------------------------------------------------- NBONDS: found 15110 intra-atom interactions NBONDS: found 15095 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =77704.444 grad(E)=215.425 E(BOND)=5257.531 E(ANGL)=42929.154 | | E(VDW )=4277.923 E(CDIH)=3854.804 E(NOE )=20885.669 E(PLAN)=499.363 | ------------------------------------------------------------------------------- NBONDS: found 15066 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =62917.595 grad(E)=112.305 E(BOND)=3119.804 E(ANGL)=29542.368 | | E(VDW )=3968.966 E(CDIH)=3899.375 E(NOE )=21886.456 E(PLAN)=500.626 | ------------------------------------------------------------------------------- NBONDS: found 15012 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =56123.659 grad(E)=92.444 E(BOND)=2350.688 E(ANGL)=24721.811 | | E(VDW )=3728.272 E(CDIH)=4054.356 E(NOE )=20779.141 E(PLAN)=489.390 | ------------------------------------------------------------------------------- NBONDS: found 14953 intra-atom interactions NBONDS: found 14843 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =51725.481 grad(E)=86.392 E(BOND)=2162.491 E(ANGL)=21436.294 | | E(VDW )=3688.720 E(CDIH)=4035.937 E(NOE )=19877.196 E(PLAN)=524.844 | ------------------------------------------------------------------------------- NBONDS: found 14799 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =48845.433 grad(E)=62.166 E(BOND)=1829.309 E(ANGL)=19685.753 | | E(VDW )=3606.377 E(CDIH)=4028.980 E(NOE )=19134.926 E(PLAN)=560.087 | ------------------------------------------------------------------------------- NBONDS: found 14684 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =46091.612 grad(E)=63.276 E(BOND)=1797.823 E(ANGL)=18610.803 | | E(VDW )=3322.258 E(CDIH)=4058.161 E(NOE )=17732.648 E(PLAN)=569.919 | ------------------------------------------------------------------------------- NBONDS: found 14635 intra-atom interactions NBONDS: found 14558 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =43496.855 grad(E)=65.236 E(BOND)=1652.104 E(ANGL)=17322.345 | | E(VDW )=3167.002 E(CDIH)=3957.594 E(NOE )=16800.700 E(PLAN)=597.110 | ------------------------------------------------------------------------------- NBONDS: found 14440 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =41381.604 grad(E)=73.918 E(BOND)=1663.894 E(ANGL)=15984.038 | | E(VDW )=3039.984 E(CDIH)=3982.941 E(NOE )=16083.989 E(PLAN)=626.759 | ------------------------------------------------------------------------------- NBONDS: found 14333 intra-atom interactions NBONDS: found 14256 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =38280.613 grad(E)=88.318 E(BOND)=1582.448 E(ANGL)=13932.342 | | E(VDW )=2767.559 E(CDIH)=3909.763 E(NOE )=15465.725 E(PLAN)=622.776 | ------------------------------------------------------------------------------- --------------- cycle= 110 ------ stepsize= 0.0001 ----------------------- | Etotal =36264.772 grad(E)=37.552 E(BOND)=1230.317 E(ANGL)=12766.293 | | E(VDW )=2639.286 E(CDIH)=3905.153 E(NOE )=15111.733 E(PLAN)=611.990 | ------------------------------------------------------------------------------- NBONDS: found 14215 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0001 ----------------------- | Etotal =35145.217 grad(E)=40.890 E(BOND)=1177.321 E(ANGL)=12274.260 | | E(VDW )=2461.878 E(CDIH)=3878.158 E(NOE )=14753.670 E(PLAN)=599.930 | ------------------------------------------------------------------------------- NBONDS: found 14084 intra-atom interactions NBONDS: found 13971 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0001 ----------------------- | Etotal =33788.142 grad(E)=65.518 E(BOND)=1247.216 E(ANGL)=11281.998 | | E(VDW )=2225.569 E(CDIH)=3827.359 E(NOE )=14612.921 E(PLAN)=593.078 | ------------------------------------------------------------------------------- --------------- cycle= 140 ------ stepsize= 0.0001 ----------------------- | Etotal =32435.749 grad(E)=38.645 E(BOND)=1193.422 E(ANGL)=10253.108 | | E(VDW )=2142.343 E(CDIH)=3773.660 E(NOE )=14475.997 E(PLAN)=597.219 | ------------------------------------------------------------------------------- NBONDS: found 13876 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =31633.622 grad(E)=31.617 E(BOND)=1146.640 E(ANGL)=9883.540 | | E(VDW )=2121.592 E(CDIH)=3738.086 E(NOE )=14150.165 E(PLAN)=593.600 | ------------------------------------------------------------------------------- --------------- cycle= 160 ------ stepsize= 0.0001 ----------------------- | Etotal =31081.645 grad(E)=32.296 E(BOND)=1174.967 E(ANGL)=9692.640 | | E(VDW )=2102.941 E(CDIH)=3668.005 E(NOE )=13866.157 E(PLAN)=576.935 | ------------------------------------------------------------------------------- NBONDS: found 13779 intra-atom interactions --------------- cycle= 170 ------ stepsize= 0.0001 ----------------------- | Etotal =30516.964 grad(E)=32.694 E(BOND)=1027.110 E(ANGL)=9521.953 | | E(VDW )=2058.711 E(CDIH)=3596.792 E(NOE )=13764.001 E(PLAN)=548.397 | ------------------------------------------------------------------------------- NBONDS: found 13618 intra-atom interactions --------------- cycle= 180 ------ stepsize= 0.0001 ----------------------- | Etotal =30039.555 grad(E)=24.096 E(BOND)=1025.238 E(ANGL)=9444.701 | | E(VDW )=1960.672 E(CDIH)=3539.784 E(NOE )=13558.441 E(PLAN)=510.718 | ------------------------------------------------------------------------------- NBONDS: found 13491 intra-atom interactions --------------- cycle= 190 ------ stepsize= 0.0001 ----------------------- | Etotal =29636.538 grad(E)=23.013 E(BOND)=995.134 E(ANGL)=9324.903 | | E(VDW )=1937.803 E(CDIH)=3503.852 E(NOE )=13400.148 E(PLAN)=474.697 | ------------------------------------------------------------------------------- NBONDS: found 13320 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =29275.992 grad(E)=21.342 E(BOND)=951.473 E(ANGL)=9127.192 | | E(VDW )=1927.594 E(CDIH)=3433.984 E(NOE )=13391.434 E(PLAN)=444.316 | ------------------------------------------------------------------------------- NBONDS: found 13180 intra-atom interactions --------------- cycle= 210 ------ stepsize= 0.0001 ----------------------- | Etotal =28911.764 grad(E)=27.016 E(BOND)=953.532 E(ANGL)=9008.138 | | E(VDW )=1894.797 E(CDIH)=3342.746 E(NOE )=13293.437 E(PLAN)=419.114 | ------------------------------------------------------------------------------- --------------- cycle= 220 ------ stepsize= 0.0001 ----------------------- | Etotal =28367.118 grad(E)=32.961 E(BOND)=953.418 E(ANGL)=8800.478 | | E(VDW )=1847.780 E(CDIH)=3289.742 E(NOE )=13081.839 E(PLAN)=393.861 | ------------------------------------------------------------------------------- NBONDS: found 13122 intra-atom interactions NBONDS: found 13045 intra-atom interactions --------------- cycle= 230 ------ stepsize= 0.0001 ----------------------- | Etotal =27662.495 grad(E)=25.126 E(BOND)=895.432 E(ANGL)=8341.241 | | E(VDW )=1783.716 E(CDIH)=3283.150 E(NOE )=12998.151 E(PLAN)=360.805 | ------------------------------------------------------------------------------- --------------- cycle= 240 ------ stepsize= 0.0001 ----------------------- | Etotal =27137.768 grad(E)=26.532 E(BOND)=918.242 E(ANGL)=7977.457 | | E(VDW )=1776.428 E(CDIH)=3252.472 E(NOE )=12853.135 E(PLAN)=360.034 | ------------------------------------------------------------------------------- NBONDS: found 13005 intra-atom interactions --------------- cycle= 250 ------ stepsize= 0.0001 ----------------------- | Etotal =26701.518 grad(E)=26.295 E(BOND)=888.681 E(ANGL)=7657.299 | | E(VDW )=1830.104 E(CDIH)=3252.647 E(NOE )=12718.406 E(PLAN)=354.382 | ------------------------------------------------------------------------------- NBONDS: found 12930 intra-atom interactions NBONDS: found 12888 intra-atom interactions --------------- cycle= 260 ------ stepsize= 0.0001 ----------------------- | Etotal =26348.872 grad(E)=24.300 E(BOND)=894.416 E(ANGL)=7437.957 | | E(VDW )=1799.802 E(CDIH)=3234.069 E(NOE )=12632.133 E(PLAN)=350.494 | ------------------------------------------------------------------------------- NBONDS: found 12818 intra-atom interactions --------------- cycle= 270 ------ stepsize= 0.0001 ----------------------- | Etotal =26080.747 grad(E)=21.288 E(BOND)=896.620 E(ANGL)=7315.064 | | E(VDW )=1750.764 E(CDIH)=3210.236 E(NOE )=12565.821 E(PLAN)=342.243 | ------------------------------------------------------------------------------- NBONDS: found 12764 intra-atom interactions --------------- cycle= 280 ------ stepsize= 0.0001 ----------------------- | Etotal =25742.197 grad(E)=24.508 E(BOND)=874.090 E(ANGL)=7219.784 | | E(VDW )=1626.181 E(CDIH)=3199.444 E(NOE )=12486.865 E(PLAN)=335.835 | ------------------------------------------------------------------------------- NBONDS: found 12682 intra-atom interactions --------------- cycle= 290 ------ stepsize= 0.0001 ----------------------- | Etotal =25392.689 grad(E)=26.428 E(BOND)=853.344 E(ANGL)=7170.501 | | E(VDW )=1483.482 E(CDIH)=3193.988 E(NOE )=12356.428 E(PLAN)=334.946 | ------------------------------------------------------------------------------- NBONDS: found 12587 intra-atom interactions --------------- cycle= 300 ------ stepsize= 0.0001 ----------------------- | Etotal =25045.247 grad(E)=22.067 E(BOND)=847.250 E(ANGL)=7067.237 | | E(VDW )=1392.978 E(CDIH)=3192.854 E(NOE )=12205.796 E(PLAN)=339.131 | ------------------------------------------------------------------------------- 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= 0.134354411E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 0.00002 -0.00001 0.00002 velocity [A/ps] : -0.01634 -0.18328 -0.17520 ang. mom. [amu A/ps] : 41911.08641 -86667.05334 303796.06669 kin. ener. [Kcal/mol] : 5.22269 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00002 -0.00001 0.00002 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 12585 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=37084.498 E(kin)=5955.198 temperature=2951.051 | | Etotal =31129.300 grad(E)=73.026 E(BOND)=84.725 E(ANGL)=706.724 | | E(DIHE)=0.000 E(IMPR)=13207.092 E(VDW )=1392.978 E(CDIH)=3192.854 | | E(NOE )=12205.796 E(PLAN)=339.131 | ------------------------------------------------------------------------------- NBONDS: found 12611 intra-atom interactions NBONDS: found 12568 intra-atom interactions NBONDS: found 12490 intra-atom interactions NBONDS: found 12413 intra-atom interactions NBONDS: found 12332 intra-atom interactions NBONDS: found 12277 intra-atom interactions NBONDS: found 12259 intra-atom interactions NBONDS: found 12253 intra-atom interactions NBONDS: found 12247 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=34424.671 E(kin)=6745.729 temperature=3342.792 | | Etotal =27678.942 grad(E)=67.023 E(BOND)=3147.468 E(ANGL)=5951.238 | | E(DIHE)=0.000 E(IMPR)=7933.383 E(VDW )=664.181 E(CDIH)=1945.571 | | E(NOE )=7875.945 E(PLAN)=161.155 | ------------------------------------------------------------------------------- NBONDS: found 12264 intra-atom interactions NBONDS: found 12276 intra-atom interactions NBONDS: found 12293 intra-atom interactions NBONDS: found 12210 intra-atom interactions NBONDS: found 12261 intra-atom interactions NBONDS: found 12273 intra-atom interactions NBONDS: found 12220 intra-atom interactions NBONDS: found 12178 intra-atom interactions NBONDS: found 12177 intra-atom interactions NBONDS: found 12131 intra-atom interactions NBONDS: found 12112 intra-atom interactions NBONDS: found 12076 intra-atom interactions NBONDS: found 12097 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=33974.563 E(kin)=6950.036 temperature=3444.035 | | Etotal =27024.526 grad(E)=67.478 E(BOND)=3051.703 E(ANGL)=6218.846 | | E(DIHE)=0.000 E(IMPR)=7240.171 E(VDW )=504.322 E(CDIH)=1586.445 | | E(NOE )=8247.666 E(PLAN)=175.374 | ------------------------------------------------------------------------------- NBONDS: found 12049 intra-atom interactions NBONDS: found 11999 intra-atom interactions NBONDS: found 11987 intra-atom interactions NBONDS: found 11957 intra-atom interactions NBONDS: found 11918 intra-atom interactions NBONDS: found 11885 intra-atom interactions NBONDS: found 11840 intra-atom interactions NBONDS: found 11834 intra-atom interactions NBONDS: found 11822 intra-atom interactions NBONDS: found 11807 intra-atom interactions NBONDS: found 11810 intra-atom interactions NBONDS: found 11762 intra-atom interactions NBONDS: found 11673 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=31555.583 E(kin)=6576.701 temperature=3259.031 | | Etotal =24978.882 grad(E)=66.662 E(BOND)=2783.880 E(ANGL)=5534.778 | | E(DIHE)=0.000 E(IMPR)=6479.454 E(VDW )=362.089 E(CDIH)=1907.779 | | E(NOE )=7747.436 E(PLAN)=163.466 | ------------------------------------------------------------------------------- NBONDS: found 11693 intra-atom interactions NBONDS: found 11647 intra-atom interactions NBONDS: found 11597 intra-atom interactions NBONDS: found 11567 intra-atom interactions NBONDS: found 11540 intra-atom interactions NBONDS: found 11511 intra-atom interactions NBONDS: found 11517 intra-atom interactions NBONDS: found 11528 intra-atom interactions NBONDS: found 11535 intra-atom interactions NBONDS: found 11534 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=30144.979 E(kin)=6260.718 temperature=3102.449 | | Etotal =23884.261 grad(E)=67.145 E(BOND)=2757.974 E(ANGL)=5355.585 | | E(DIHE)=0.000 E(IMPR)=5895.799 E(VDW )=280.923 E(CDIH)=1622.903 | | E(NOE )=7841.027 E(PLAN)=130.050 | ------------------------------------------------------------------------------- NBONDS: found 11518 intra-atom interactions NBONDS: found 11519 intra-atom interactions NBONDS: found 11490 intra-atom interactions NBONDS: found 11446 intra-atom interactions NBONDS: found 11409 intra-atom interactions NBONDS: found 11382 intra-atom interactions NBONDS: found 11359 intra-atom interactions NBONDS: found 11323 intra-atom interactions NBONDS: found 11345 intra-atom interactions NBONDS: found 11378 intra-atom interactions NBONDS: found 11371 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=28932.168 E(kin)=6368.262 temperature=3155.741 | | Etotal =22563.906 grad(E)=66.422 E(BOND)=2442.097 E(ANGL)=5475.043 | | E(DIHE)=0.000 E(IMPR)=5369.140 E(VDW )=311.390 E(CDIH)=1664.525 | | E(NOE )=7098.088 E(PLAN)=203.623 | ------------------------------------------------------------------------------- NBONDS: found 11365 intra-atom interactions NBONDS: found 11371 intra-atom interactions NBONDS: found 11390 intra-atom interactions NBONDS: found 11459 intra-atom interactions NBONDS: found 11504 intra-atom interactions NBONDS: found 11464 intra-atom interactions NBONDS: found 11474 intra-atom interactions NBONDS: found 11474 intra-atom interactions NBONDS: found 11491 intra-atom interactions NBONDS: found 11517 intra-atom interactions NBONDS: found 11554 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=27720.736 E(kin)=6270.215 temperature=3107.155 | | Etotal =21450.521 grad(E)=66.265 E(BOND)=2526.943 E(ANGL)=4950.066 | | E(DIHE)=0.000 E(IMPR)=5189.117 E(VDW )=239.177 E(CDIH)=1421.559 | | E(NOE )=6900.008 E(PLAN)=223.651 | ------------------------------------------------------------------------------- NBONDS: found 11588 intra-atom interactions NBONDS: found 11599 intra-atom interactions NBONDS: found 11604 intra-atom interactions NBONDS: found 11587 intra-atom interactions NBONDS: found 11608 intra-atom interactions NBONDS: found 11604 intra-atom interactions NBONDS: found 11588 intra-atom interactions NBONDS: found 11566 intra-atom interactions NBONDS: found 11554 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=26901.981 E(kin)=6145.036 temperature=3045.123 | | Etotal =20756.945 grad(E)=66.381 E(BOND)=2465.488 E(ANGL)=4672.453 | | E(DIHE)=0.000 E(IMPR)=5131.070 E(VDW )=242.090 E(CDIH)=1374.389 | | E(NOE )=6682.266 E(PLAN)=189.189 | ------------------------------------------------------------------------------- NBONDS: found 11511 intra-atom interactions NBONDS: found 11523 intra-atom interactions NBONDS: found 11467 intra-atom interactions NBONDS: found 11483 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00002 -0.00001 0.00002 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] : 0.00002 -0.00001 0.00002 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] : 0.00002 -0.00001 0.00002 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 11422 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=38915.202 E(kin)=6350.445 temperature=3146.912 | | Etotal =32564.757 grad(E)=122.888 E(BOND)=4847.048 E(ANGL)=9341.193 | | E(DIHE)=0.000 E(IMPR)=9785.132 E(VDW )=289.729 E(CDIH)=1484.302 | | E(NOE )=6629.075 E(PLAN)=188.278 | ------------------------------------------------------------------------------- NBONDS: found 11428 intra-atom interactions NBONDS: found 11406 intra-atom interactions NBONDS: found 11339 intra-atom interactions NBONDS: found 11264 intra-atom interactions NBONDS: found 11276 intra-atom interactions NBONDS: found 11311 intra-atom interactions NBONDS: found 11281 intra-atom interactions NBONDS: found 11320 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=34366.798 E(kin)=6239.059 temperature=3091.716 | | Etotal =28127.740 grad(E)=95.588 E(BOND)=2845.732 E(ANGL)=6824.571 | | E(DIHE)=0.000 E(IMPR)=8517.397 E(VDW )=360.417 E(CDIH)=1570.294 | | E(NOE )=7787.093 E(PLAN)=222.236 | ------------------------------------------------------------------------------- NBONDS: found 11345 intra-atom interactions NBONDS: found 11322 intra-atom interactions NBONDS: found 11338 intra-atom interactions NBONDS: found 11335 intra-atom interactions NBONDS: found 11364 intra-atom interactions NBONDS: found 11341 intra-atom interactions NBONDS: found 11335 intra-atom interactions NBONDS: found 11351 intra-atom interactions NBONDS: found 11325 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=33376.355 E(kin)=6378.865 temperature=3160.995 | | Etotal =26997.490 grad(E)=93.634 E(BOND)=2964.090 E(ANGL)=6305.980 | | E(DIHE)=0.000 E(IMPR)=8044.823 E(VDW )=389.320 E(CDIH)=1552.483 | | E(NOE )=7533.636 E(PLAN)=207.158 | ------------------------------------------------------------------------------- NBONDS: found 11343 intra-atom interactions NBONDS: found 11323 intra-atom interactions NBONDS: found 11339 intra-atom interactions NBONDS: found 11360 intra-atom interactions NBONDS: found 11343 intra-atom interactions NBONDS: found 11336 intra-atom interactions NBONDS: found 11311 intra-atom interactions NBONDS: found 11321 intra-atom interactions NBONDS: found 11381 intra-atom interactions NBONDS: found 11393 intra-atom interactions NBONDS: found 11372 intra-atom interactions NBONDS: found 11377 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=33303.103 E(kin)=6573.060 temperature=3257.227 | | Etotal =26730.043 grad(E)=92.949 E(BOND)=2709.766 E(ANGL)=6004.988 | | E(DIHE)=0.000 E(IMPR)=8093.755 E(VDW )=438.389 E(CDIH)=1496.878 | | E(NOE )=7763.651 E(PLAN)=222.616 | ------------------------------------------------------------------------------- NBONDS: found 11429 intra-atom interactions NBONDS: found 11422 intra-atom interactions NBONDS: found 11421 intra-atom interactions NBONDS: found 11460 intra-atom interactions NBONDS: found 11480 intra-atom interactions NBONDS: found 11430 intra-atom interactions NBONDS: found 11434 intra-atom interactions NBONDS: found 11480 intra-atom interactions NBONDS: found 11469 intra-atom interactions NBONDS: found 11483 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=32653.698 E(kin)=6423.175 temperature=3182.953 | | Etotal =26230.523 grad(E)=90.940 E(BOND)=2889.002 E(ANGL)=6112.611 | | E(DIHE)=0.000 E(IMPR)=7638.002 E(VDW )=393.961 E(CDIH)=1497.533 | | E(NOE )=7515.469 E(PLAN)=183.947 | ------------------------------------------------------------------------------- NBONDS: found 11484 intra-atom interactions NBONDS: found 11473 intra-atom interactions NBONDS: found 11472 intra-atom interactions NBONDS: found 11444 intra-atom interactions NBONDS: found 11457 intra-atom interactions NBONDS: found 11465 intra-atom interactions NBONDS: found 11430 intra-atom interactions NBONDS: found 11442 intra-atom interactions NBONDS: found 11396 intra-atom interactions NBONDS: found 11405 intra-atom interactions NBONDS: found 11366 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=32863.361 E(kin)=6311.346 temperature=3127.537 | | Etotal =26552.014 grad(E)=97.705 E(BOND)=3038.562 E(ANGL)=5657.768 | | E(DIHE)=0.000 E(IMPR)=7722.331 E(VDW )=409.983 E(CDIH)=1425.366 | | E(NOE )=8107.565 E(PLAN)=190.440 | ------------------------------------------------------------------------------- NBONDS: found 11373 intra-atom interactions NBONDS: found 11395 intra-atom interactions NBONDS: found 11389 intra-atom interactions NBONDS: found 11414 intra-atom interactions NBONDS: found 11437 intra-atom interactions NBONDS: found 11410 intra-atom interactions NBONDS: found 11417 intra-atom interactions NBONDS: found 11384 intra-atom interactions NBONDS: found 11389 intra-atom interactions NBONDS: found 11379 intra-atom interactions NBONDS: found 11359 intra-atom interactions NBONDS: found 11369 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=32294.383 E(kin)=6196.873 temperature=3070.811 | | Etotal =26097.510 grad(E)=90.903 E(BOND)=2380.079 E(ANGL)=6264.880 | | E(DIHE)=0.000 E(IMPR)=7980.930 E(VDW )=371.913 E(CDIH)=1309.211 | | E(NOE )=7555.153 E(PLAN)=235.345 | ------------------------------------------------------------------------------- NBONDS: found 11333 intra-atom interactions NBONDS: found 11310 intra-atom interactions NBONDS: found 11397 intra-atom interactions NBONDS: found 11464 intra-atom interactions NBONDS: found 11449 intra-atom interactions NBONDS: found 11435 intra-atom interactions NBONDS: found 11477 intra-atom interactions NBONDS: found 11521 intra-atom interactions NBONDS: found 11520 intra-atom interactions NBONDS: found 11532 intra-atom interactions NBONDS: found 11536 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=32541.084 E(kin)=6263.803 temperature=3103.977 | | Etotal =26277.281 grad(E)=92.483 E(BOND)=2587.118 E(ANGL)=6118.251 | | E(DIHE)=0.000 E(IMPR)=7476.011 E(VDW )=452.124 E(CDIH)=1389.588 | | E(NOE )=8097.664 E(PLAN)=156.525 | ------------------------------------------------------------------------------- NBONDS: found 11516 intra-atom interactions NBONDS: found 11498 intra-atom interactions NBONDS: found 11519 intra-atom interactions NBONDS: found 11507 intra-atom interactions NBONDS: found 11551 intra-atom interactions NBONDS: found 11552 intra-atom interactions NBONDS: found 11534 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00002 -0.00001 0.00002 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] : 0.00002 -0.00001 0.00002 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] : 0.00002 -0.00001 0.00002 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 11539 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=39586.123 E(kin)=6375.839 temperature=3159.496 | | Etotal =33210.284 grad(E)=104.395 E(BOND)=2620.924 E(ANGL)=6120.110 | | E(DIHE)=0.000 E(IMPR)=14834.503 E(VDW )=355.869 E(CDIH)=1358.224 | | E(NOE )=7686.353 E(PLAN)=234.300 | ------------------------------------------------------------------------------- NBONDS: found 11569 intra-atom interactions NBONDS: found 11571 intra-atom interactions NBONDS: found 11585 intra-atom interactions NBONDS: found 11642 intra-atom interactions NBONDS: found 11712 intra-atom interactions NBONDS: found 11787 intra-atom interactions NBONDS: found 11810 intra-atom interactions NBONDS: found 11833 intra-atom interactions NBONDS: found 11890 intra-atom interactions NBONDS: found 11917 intra-atom interactions NBONDS: found 11960 intra-atom interactions NBONDS: found 12016 intra-atom interactions NBONDS: found 12088 intra-atom interactions NBONDS: found 12148 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=33403.801 E(kin)=7450.619 temperature=3692.094 | | Etotal =25953.183 grad(E)=103.822 E(BOND)=3121.030 E(ANGL)=7503.401 | | E(DIHE)=0.000 E(IMPR)=3952.725 E(VDW )=439.916 E(CDIH)=2309.011 | | E(NOE )=8335.228 E(PLAN)=291.871 | ------------------------------------------------------------------------------- NBONDS: found 12195 intra-atom interactions NBONDS: found 12233 intra-atom interactions NBONDS: found 12218 intra-atom interactions NBONDS: found 12267 intra-atom interactions NBONDS: found 12352 intra-atom interactions NBONDS: found 12491 intra-atom interactions NBONDS: found 12604 intra-atom interactions NBONDS: found 12692 intra-atom interactions NBONDS: found 12780 intra-atom interactions NBONDS: found 12837 intra-atom interactions NBONDS: found 12894 intra-atom interactions NBONDS: found 12848 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=29399.702 E(kin)=6375.391 temperature=3159.274 | | Etotal =23024.311 grad(E)=89.084 E(BOND)=2933.080 E(ANGL)=6727.291 | | E(DIHE)=0.000 E(IMPR)=1815.298 E(VDW )=492.184 E(CDIH)=2050.989 | | E(NOE )=8695.037 E(PLAN)=310.432 | ------------------------------------------------------------------------------- NBONDS: found 12884 intra-atom interactions NBONDS: found 12974 intra-atom interactions NBONDS: found 12960 intra-atom interactions NBONDS: found 12960 intra-atom interactions NBONDS: found 12968 intra-atom interactions NBONDS: found 13011 intra-atom interactions NBONDS: found 13065 intra-atom interactions NBONDS: found 13092 intra-atom interactions NBONDS: found 13132 intra-atom interactions NBONDS: found 13158 intra-atom interactions NBONDS: found 13232 intra-atom interactions NBONDS: found 13314 intra-atom interactions NBONDS: found 13410 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=28172.213 E(kin)=6293.365 temperature=3118.627 | | Etotal =21878.849 grad(E)=94.027 E(BOND)=2752.354 E(ANGL)=5835.583 | | E(DIHE)=0.000 E(IMPR)=1811.056 E(VDW )=507.030 E(CDIH)=2059.075 | | E(NOE )=8560.607 E(PLAN)=353.143 | ------------------------------------------------------------------------------- NBONDS: found 13466 intra-atom interactions NBONDS: found 13497 intra-atom interactions NBONDS: found 13519 intra-atom interactions NBONDS: found 13512 intra-atom interactions NBONDS: found 13509 intra-atom interactions NBONDS: found 13501 intra-atom interactions NBONDS: found 13467 intra-atom interactions NBONDS: found 13463 intra-atom interactions NBONDS: found 13485 intra-atom interactions NBONDS: found 13439 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=26831.766 E(kin)=6464.266 temperature=3203.315 | | Etotal =20367.499 grad(E)=87.473 E(BOND)=2249.676 E(ANGL)=5588.607 | | E(DIHE)=0.000 E(IMPR)=1534.831 E(VDW )=507.855 E(CDIH)=1697.547 | | E(NOE )=8499.264 E(PLAN)=289.720 | ------------------------------------------------------------------------------- NBONDS: found 13428 intra-atom interactions NBONDS: found 13442 intra-atom interactions NBONDS: found 13491 intra-atom interactions NBONDS: found 13549 intra-atom interactions NBONDS: found 13582 intra-atom interactions NBONDS: found 13629 intra-atom interactions NBONDS: found 13616 intra-atom interactions NBONDS: found 13655 intra-atom interactions NBONDS: found 13666 intra-atom interactions NBONDS: found 13688 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=26219.854 E(kin)=6158.091 temperature=3051.592 | | Etotal =20061.763 grad(E)=86.977 E(BOND)=2256.986 E(ANGL)=5304.704 | | E(DIHE)=0.000 E(IMPR)=1546.956 E(VDW )=516.501 E(CDIH)=1731.470 | | E(NOE )=8433.957 E(PLAN)=271.189 | ------------------------------------------------------------------------------- NBONDS: found 13640 intra-atom interactions NBONDS: found 13637 intra-atom interactions NBONDS: found 13650 intra-atom interactions NBONDS: found 13703 intra-atom interactions NBONDS: found 13696 intra-atom interactions NBONDS: found 13699 intra-atom interactions NBONDS: found 13705 intra-atom interactions NBONDS: found 13748 intra-atom interactions NBONDS: found 13806 intra-atom interactions NBONDS: found 13824 intra-atom interactions NBONDS: found 13891 intra-atom interactions NBONDS: found 13895 intra-atom interactions NBONDS: found 13914 intra-atom interactions NBONDS: found 13938 intra-atom interactions NBONDS: found 13928 intra-atom interactions NBONDS: found 13966 intra-atom interactions NBONDS: found 13957 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=26672.705 E(kin)=6162.036 temperature=3053.548 | | Etotal =20510.669 grad(E)=95.224 E(BOND)=2510.991 E(ANGL)=5580.756 | | E(DIHE)=0.000 E(IMPR)=1775.736 E(VDW )=540.928 E(CDIH)=1723.902 | | E(NOE )=8090.678 E(PLAN)=287.680 | ------------------------------------------------------------------------------- NBONDS: found 13964 intra-atom interactions NBONDS: found 14039 intra-atom interactions NBONDS: found 14124 intra-atom interactions NBONDS: found 14155 intra-atom interactions NBONDS: found 14169 intra-atom interactions NBONDS: found 14219 intra-atom interactions NBONDS: found 14265 intra-atom interactions NBONDS: found 14301 intra-atom interactions NBONDS: found 14323 intra-atom interactions NBONDS: found 14350 intra-atom interactions NBONDS: found 14361 intra-atom interactions NBONDS: found 14276 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=25876.881 E(kin)=6325.951 temperature=3134.774 | | Etotal =19550.930 grad(E)=88.768 E(BOND)=2529.554 E(ANGL)=5144.227 | | E(DIHE)=0.000 E(IMPR)=1475.979 E(VDW )=540.033 E(CDIH)=1728.547 | | E(NOE )=7856.317 E(PLAN)=276.273 | ------------------------------------------------------------------------------- NBONDS: found 14321 intra-atom interactions NBONDS: found 14361 intra-atom interactions NBONDS: found 14463 intra-atom interactions NBONDS: found 14478 intra-atom interactions NBONDS: found 14485 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00002 -0.00001 0.00002 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] : 0.00002 -0.00001 0.00002 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] : 0.00002 -0.00001 0.00002 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 13177 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=34258.509 E(kin)=6240.109 temperature=3092.236 | | Etotal =28018.399 grad(E)=170.263 E(BOND)=5063.619 E(ANGL)=9892.488 | | E(DIHE)=0.000 E(IMPR)=3007.170 E(VDW )=104.880 E(CDIH)=1639.127 | | E(NOE )=8023.689 E(PLAN)=287.427 | ------------------------------------------------------------------------------- NBONDS: found 13244 intra-atom interactions NBONDS: found 13306 intra-atom interactions NBONDS: found 13411 intra-atom interactions NBONDS: found 13512 intra-atom interactions NBONDS: found 13528 intra-atom interactions NBONDS: found 13565 intra-atom interactions NBONDS: found 13626 intra-atom interactions NBONDS: found 13678 intra-atom interactions NBONDS: found 13793 intra-atom interactions NBONDS: found 13833 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=29853.005 E(kin)=6424.112 temperature=3183.417 | | Etotal =23428.893 grad(E)=126.997 E(BOND)=2820.063 E(ANGL)=6977.369 | | E(DIHE)=0.000 E(IMPR)=1887.301 E(VDW )=111.731 E(CDIH)=1856.006 | | E(NOE )=9428.715 E(PLAN)=347.709 | ------------------------------------------------------------------------------- NBONDS: found 13932 intra-atom interactions NBONDS: found 14026 intra-atom interactions NBONDS: found 14105 intra-atom interactions NBONDS: found 14155 intra-atom interactions NBONDS: found 14208 intra-atom interactions NBONDS: found 14407 intra-atom interactions NBONDS: found 14501 intra-atom interactions NBONDS: found 14553 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=29176.539 E(kin)=6274.193 temperature=3109.126 | | Etotal =22902.346 grad(E)=122.694 E(BOND)=2802.668 E(ANGL)=6290.243 | | E(DIHE)=0.000 E(IMPR)=1894.250 E(VDW )=122.323 E(CDIH)=1909.440 | | E(NOE )=9493.992 E(PLAN)=389.430 | ------------------------------------------------------------------------------- NBONDS: found 14679 intra-atom interactions NBONDS: found 14740 intra-atom interactions NBONDS: found 14787 intra-atom interactions NBONDS: found 14851 intra-atom interactions NBONDS: found 14880 intra-atom interactions NBONDS: found 14970 intra-atom interactions NBONDS: found 14977 intra-atom interactions NBONDS: found 15016 intra-atom interactions NBONDS: found 15031 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=28959.520 E(kin)=6225.903 temperature=3085.196 | | Etotal =22733.617 grad(E)=123.917 E(BOND)=2627.942 E(ANGL)=6629.255 | | E(DIHE)=0.000 E(IMPR)=2097.068 E(VDW )=129.179 E(CDIH)=1817.718 | | E(NOE )=9084.058 E(PLAN)=348.397 | ------------------------------------------------------------------------------- NBONDS: found 15027 intra-atom interactions NBONDS: found 15084 intra-atom interactions NBONDS: found 15054 intra-atom interactions NBONDS: found 15112 intra-atom interactions NBONDS: found 15166 intra-atom interactions NBONDS: found 15212 intra-atom interactions NBONDS: found 15307 intra-atom interactions NBONDS: found 15329 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=28847.568 E(kin)=6273.005 temperature=3108.537 | | Etotal =22574.563 grad(E)=121.284 E(BOND)=2687.557 E(ANGL)=6533.109 | | E(DIHE)=0.000 E(IMPR)=1787.588 E(VDW )=135.981 E(CDIH)=1897.476 | | E(NOE )=9104.326 E(PLAN)=428.527 | ------------------------------------------------------------------------------- NBONDS: found 15376 intra-atom interactions NBONDS: found 15418 intra-atom interactions NBONDS: found 15465 intra-atom interactions NBONDS: found 15533 intra-atom interactions NBONDS: found 15619 intra-atom interactions NBONDS: found 15788 intra-atom interactions NBONDS: found 15892 intra-atom interactions NBONDS: found 16011 intra-atom interactions NBONDS: found 16075 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=28892.444 E(kin)=6061.772 temperature=3003.863 | | Etotal =22830.672 grad(E)=123.103 E(BOND)=2716.302 E(ANGL)=6679.499 | | E(DIHE)=0.000 E(IMPR)=1740.237 E(VDW )=155.909 E(CDIH)=1643.877 | | E(NOE )=9539.981 E(PLAN)=354.866 | ------------------------------------------------------------------------------- NBONDS: found 16236 intra-atom interactions NBONDS: found 16325 intra-atom interactions NBONDS: found 16385 intra-atom interactions NBONDS: found 16415 intra-atom interactions NBONDS: found 16542 intra-atom interactions NBONDS: found 16622 intra-atom interactions NBONDS: found 16671 intra-atom interactions NBONDS: found 16736 intra-atom interactions NBONDS: found 16898 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=28524.150 E(kin)=5963.521 temperature=2955.175 | | Etotal =22560.629 grad(E)=124.672 E(BOND)=2525.078 E(ANGL)=6636.123 | | E(DIHE)=0.000 E(IMPR)=1912.737 E(VDW )=178.515 E(CDIH)=1701.431 | | E(NOE )=9249.410 E(PLAN)=357.334 | ------------------------------------------------------------------------------- NBONDS: found 17050 intra-atom interactions NBONDS: found 17234 intra-atom interactions NBONDS: found 17453 intra-atom interactions NBONDS: found 17629 intra-atom interactions NBONDS: found 17777 intra-atom interactions NBONDS: found 17906 intra-atom interactions NBONDS: found 18019 intra-atom interactions NBONDS: found 18132 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=28773.840 E(kin)=6030.758 temperature=2988.494 | | Etotal =22743.082 grad(E)=123.400 E(BOND)=2483.298 E(ANGL)=6831.397 | | E(DIHE)=0.000 E(IMPR)=1961.060 E(VDW )=195.869 E(CDIH)=1829.565 | | E(NOE )=9079.341 E(PLAN)=362.551 | ------------------------------------------------------------------------------- NBONDS: found 18192 intra-atom interactions NBONDS: found 18340 intra-atom interactions NBONDS: found 18390 intra-atom interactions NBONDS: found 18359 intra-atom interactions NBONDS: found 18451 intra-atom interactions NBONDS: found 18562 intra-atom interactions NBONDS: found 18600 intra-atom interactions --------------- step= 800 at 1.60000 ps -------------------------------- | E(kin)+E(total)=28411.436 E(kin)=6063.125 temperature=3004.533 | | Etotal =22348.311 grad(E)=124.277 E(BOND)=2448.843 E(ANGL)=6176.333 | | E(DIHE)=0.000 E(IMPR)=2186.152 E(VDW )=200.420 E(CDIH)=1663.941 | | E(NOE )=9293.368 E(PLAN)=379.254 | ------------------------------------------------------------------------------- NBONDS: found 18712 intra-atom interactions NBONDS: found 18933 intra-atom interactions NBONDS: found 19038 intra-atom interactions NBONDS: found 19105 intra-atom interactions NBONDS: found 19112 intra-atom interactions NBONDS: found 19207 intra-atom interactions NBONDS: found 19410 intra-atom interactions NBONDS: found 19538 intra-atom interactions --------------- step= 900 at 1.80000 ps -------------------------------- | E(kin)+E(total)=28488.986 E(kin)=5964.363 temperature=2955.592 | | Etotal =22524.623 grad(E)=125.969 E(BOND)=2743.391 E(ANGL)=6376.873 | | E(DIHE)=0.000 E(IMPR)=1750.864 E(VDW )=222.904 E(CDIH)=1778.510 | | E(NOE )=9348.616 E(PLAN)=303.465 | ------------------------------------------------------------------------------- NBONDS: found 19612 intra-atom interactions NBONDS: found 19732 intra-atom interactions NBONDS: found 19875 intra-atom interactions NBONDS: found 20070 intra-atom interactions NBONDS: found 20230 intra-atom interactions NBONDS: found 20409 intra-atom interactions NBONDS: found 20512 intra-atom interactions --------------- step= 1000 at 2.00000 ps -------------------------------- | E(kin)+E(total)=28405.966 E(kin)=5877.660 temperature=2912.627 | | Etotal =22528.306 grad(E)=125.797 E(BOND)=2706.076 E(ANGL)=6568.405 | | E(DIHE)=0.000 E(IMPR)=1821.443 E(VDW )=241.893 E(CDIH)=1697.041 | | E(NOE )=9103.378 E(PLAN)=390.072 | ------------------------------------------------------------------------------- NBONDS: found 20584 intra-atom interactions NBONDS: found 20631 intra-atom interactions NBONDS: found 20674 intra-atom interactions NBONDS: found 20792 intra-atom interactions NBONDS: found 20881 intra-atom interactions NBONDS: found 20951 intra-atom interactions NBONDS: found 21024 intra-atom interactions NBONDS: found 21178 intra-atom interactions --------------- step= 1100 at 2.20000 ps -------------------------------- | E(kin)+E(total)=28636.459 E(kin)=5825.060 temperature=2886.562 | | Etotal =22811.399 grad(E)=129.677 E(BOND)=2571.251 E(ANGL)=6594.572 | | E(DIHE)=0.000 E(IMPR)=1885.746 E(VDW )=245.410 E(CDIH)=1808.823 | | E(NOE )=9315.570 E(PLAN)=390.027 | ------------------------------------------------------------------------------- NBONDS: found 21252 intra-atom interactions NBONDS: found 21281 intra-atom interactions NBONDS: found 21349 intra-atom interactions NBONDS: found 21339 intra-atom interactions NBONDS: found 21328 intra-atom interactions NBONDS: found 21368 intra-atom interactions NBONDS: found 21595 intra-atom interactions --------------- step= 1200 at 2.40000 ps -------------------------------- | E(kin)+E(total)=28509.352 E(kin)=6155.125 temperature=3050.123 | | Etotal =22354.227 grad(E)=121.979 E(BOND)=2529.895 E(ANGL)=6451.392 | | E(DIHE)=0.000 E(IMPR)=1613.577 E(VDW )=251.248 E(CDIH)=1677.934 | | E(NOE )=9487.032 E(PLAN)=343.148 | ------------------------------------------------------------------------------- NBONDS: found 21792 intra-atom interactions NBONDS: found 21831 intra-atom interactions NBONDS: found 21890 intra-atom interactions NBONDS: found 22019 intra-atom interactions NBONDS: found 22135 intra-atom interactions NBONDS: found 22193 intra-atom interactions NBONDS: found 22293 intra-atom interactions NBONDS: found 22243 intra-atom interactions --------------- step= 1300 at 2.60000 ps -------------------------------- | E(kin)+E(total)=28625.889 E(kin)=6071.179 temperature=3008.524 | | Etotal =22554.710 grad(E)=125.832 E(BOND)=2684.892 E(ANGL)=6662.850 | | E(DIHE)=0.000 E(IMPR)=1817.954 E(VDW )=256.817 E(CDIH)=1753.695 | | E(NOE )=9006.443 E(PLAN)=372.059 | ------------------------------------------------------------------------------- NBONDS: found 22204 intra-atom interactions NBONDS: found 22265 intra-atom interactions NBONDS: found 22276 intra-atom interactions NBONDS: found 22269 intra-atom interactions NBONDS: found 22256 intra-atom interactions NBONDS: found 22189 intra-atom interactions NBONDS: found 22287 intra-atom interactions NBONDS: found 22364 intra-atom interactions --------------- step= 1400 at 2.80000 ps -------------------------------- | E(kin)+E(total)=28663.802 E(kin)=6233.319 temperature=3088.871 | | Etotal =22430.483 grad(E)=125.495 E(BOND)=2644.563 E(ANGL)=6687.141 | | E(DIHE)=0.000 E(IMPR)=1737.993 E(VDW )=254.672 E(CDIH)=1639.713 | | E(NOE )=9084.236 E(PLAN)=382.165 | ------------------------------------------------------------------------------- NBONDS: found 22394 intra-atom interactions NBONDS: found 22449 intra-atom interactions NBONDS: found 22536 intra-atom interactions NBONDS: found 22634 intra-atom interactions NBONDS: found 22754 intra-atom interactions NBONDS: found 22752 intra-atom interactions NBONDS: found 22625 intra-atom interactions --------------- step= 1500 at 3.00000 ps -------------------------------- | E(kin)+E(total)=28515.530 E(kin)=6004.836 temperature=2975.648 | | Etotal =22510.693 grad(E)=121.805 E(BOND)=2554.654 E(ANGL)=6679.324 | | E(DIHE)=0.000 E(IMPR)=1690.370 E(VDW )=259.610 E(CDIH)=1716.697 | | E(NOE )=9249.769 E(PLAN)=360.269 | ------------------------------------------------------------------------------- NBONDS: found 22519 intra-atom interactions NBONDS: found 22479 intra-atom interactions NBONDS: found 22378 intra-atom interactions NBONDS: found 22302 intra-atom interactions NBONDS: found 22179 intra-atom interactions NBONDS: found 22129 intra-atom interactions NBONDS: found 22198 intra-atom interactions --------------- step= 1600 at 3.20000 ps -------------------------------- | E(kin)+E(total)=28586.319 E(kin)=6046.721 temperature=2996.404 | | Etotal =22539.598 grad(E)=127.137 E(BOND)=2647.722 E(ANGL)=6673.043 | | E(DIHE)=0.000 E(IMPR)=2020.558 E(VDW )=248.811 E(CDIH)=1713.440 | | E(NOE )=8897.889 E(PLAN)=338.135 | ------------------------------------------------------------------------------- NBONDS: found 22273 intra-atom interactions NBONDS: found 22340 intra-atom interactions NBONDS: found 22374 intra-atom interactions NBONDS: found 22480 intra-atom interactions NBONDS: found 22516 intra-atom interactions NBONDS: found 22643 intra-atom interactions NBONDS: found 22765 intra-atom interactions NBONDS: found 22885 intra-atom interactions --------------- step= 1700 at 3.40000 ps -------------------------------- | E(kin)+E(total)=28424.455 E(kin)=5886.288 temperature=2916.903 | | Etotal =22538.167 grad(E)=127.127 E(BOND)=2702.240 E(ANGL)=6591.496 | | E(DIHE)=0.000 E(IMPR)=1708.022 E(VDW )=256.425 E(CDIH)=1700.733 | | E(NOE )=9195.999 E(PLAN)=383.253 | ------------------------------------------------------------------------------- NBONDS: found 22944 intra-atom interactions NBONDS: found 23020 intra-atom interactions NBONDS: found 23080 intra-atom interactions NBONDS: found 23006 intra-atom interactions NBONDS: found 23007 intra-atom interactions NBONDS: found 23018 intra-atom interactions NBONDS: found 23045 intra-atom interactions --------------- step= 1800 at 3.60000 ps -------------------------------- | E(kin)+E(total)=28578.786 E(kin)=5937.664 temperature=2942.362 | | Etotal =22641.121 grad(E)=123.260 E(BOND)=2933.245 E(ANGL)=6290.723 | | E(DIHE)=0.000 E(IMPR)=1895.259 E(VDW )=265.192 E(CDIH)=1628.313 | | E(NOE )=9239.128 E(PLAN)=389.260 | ------------------------------------------------------------------------------- NBONDS: found 22990 intra-atom interactions NBONDS: found 23028 intra-atom interactions NBONDS: found 23112 intra-atom interactions NBONDS: found 23202 intra-atom interactions NBONDS: found 23264 intra-atom interactions NBONDS: found 23310 intra-atom interactions NBONDS: found 23301 intra-atom interactions --------------- step= 1900 at 3.80000 ps -------------------------------- | E(kin)+E(total)=28856.033 E(kin)=5929.046 temperature=2938.091 | | Etotal =22926.987 grad(E)=127.523 E(BOND)=2740.095 E(ANGL)=6850.166 | | E(DIHE)=0.000 E(IMPR)=1746.591 E(VDW )=275.206 E(CDIH)=1742.156 | | E(NOE )=9161.767 E(PLAN)=411.005 | ------------------------------------------------------------------------------- NBONDS: found 23313 intra-atom interactions NBONDS: found 23280 intra-atom interactions NBONDS: found 23255 intra-atom interactions NBONDS: found 23290 intra-atom interactions NBONDS: found 23379 intra-atom interactions NBONDS: found 23343 intra-atom interactions NBONDS: found 23341 intra-atom interactions NBONDS: found 23400 intra-atom interactions --------------- step= 2000 at 4.00000 ps -------------------------------- | E(kin)+E(total)=28899.507 E(kin)=5955.609 temperature=2951.254 | | Etotal =22943.898 grad(E)=128.187 E(BOND)=2567.331 E(ANGL)=6528.468 | | E(DIHE)=0.000 E(IMPR)=2143.336 E(VDW )=277.873 E(CDIH)=1768.481 | | E(NOE )=9235.348 E(PLAN)=423.061 | ------------------------------------------------------------------------------- NBONDS: found 23550 intra-atom interactions NBONDS: found 23647 intra-atom interactions NBONDS: found 23736 intra-atom interactions NBONDS: found 23865 intra-atom interactions NBONDS: found 23902 intra-atom interactions NBONDS: found 23934 intra-atom interactions NBONDS: found 23994 intra-atom interactions NBONDS: found 24162 intra-atom interactions --------------- step= 2100 at 4.20000 ps -------------------------------- | E(kin)+E(total)=28861.817 E(kin)=5824.515 temperature=2886.292 | | Etotal =23037.302 grad(E)=126.900 E(BOND)=2794.029 E(ANGL)=6566.873 | | E(DIHE)=0.000 E(IMPR)=1985.585 E(VDW )=287.844 E(CDIH)=1836.406 | | E(NOE )=9162.575 E(PLAN)=403.990 | ------------------------------------------------------------------------------- NBONDS: found 24265 intra-atom interactions NBONDS: found 24321 intra-atom interactions NBONDS: found 24439 intra-atom interactions NBONDS: found 24424 intra-atom interactions NBONDS: found 24458 intra-atom interactions NBONDS: found 24379 intra-atom interactions NBONDS: found 24280 intra-atom interactions --------------- step= 2200 at 4.40000 ps -------------------------------- | E(kin)+E(total)=28945.526 E(kin)=5798.692 temperature=2873.495 | | Etotal =23146.834 grad(E)=126.761 E(BOND)=2615.813 E(ANGL)=6650.012 | | E(DIHE)=0.000 E(IMPR)=1967.277 E(VDW )=288.306 E(CDIH)=1832.426 | | E(NOE )=9403.173 E(PLAN)=389.827 | ------------------------------------------------------------------------------- NBONDS: found 24316 intra-atom interactions NBONDS: found 24200 intra-atom interactions NBONDS: found 24180 intra-atom interactions NBONDS: found 24212 intra-atom interactions NBONDS: found 24193 intra-atom interactions NBONDS: found 24095 intra-atom interactions NBONDS: found 23997 intra-atom interactions NBONDS: found 23972 intra-atom interactions NBONDS: found 23940 intra-atom interactions --------------- step= 2300 at 4.60000 ps -------------------------------- | E(kin)+E(total)=28842.696 E(kin)=6107.866 temperature=3026.704 | | Etotal =22734.830 grad(E)=123.701 E(BOND)=2705.556 E(ANGL)=6807.173 | | E(DIHE)=0.000 E(IMPR)=1905.102 E(VDW )=281.548 E(CDIH)=1787.824 | | E(NOE )=8882.123 E(PLAN)=365.503 | ------------------------------------------------------------------------------- NBONDS: found 23979 intra-atom interactions NBONDS: found 23942 intra-atom interactions NBONDS: found 23863 intra-atom interactions NBONDS: found 23842 intra-atom interactions NBONDS: found 23697 intra-atom interactions NBONDS: found 23539 intra-atom interactions NBONDS: found 23441 intra-atom interactions --------------- step= 2400 at 4.80000 ps -------------------------------- | E(kin)+E(total)=28864.141 E(kin)=6199.342 temperature=3072.034 | | Etotal =22664.799 grad(E)=122.394 E(BOND)=2678.859 E(ANGL)=6537.169 | | E(DIHE)=0.000 E(IMPR)=1766.912 E(VDW )=273.785 E(CDIH)=1694.336 | | E(NOE )=9267.149 E(PLAN)=446.590 | ------------------------------------------------------------------------------- NBONDS: found 23399 intra-atom interactions NBONDS: found 23218 intra-atom interactions NBONDS: found 23167 intra-atom interactions NBONDS: found 23057 intra-atom interactions NBONDS: found 23068 intra-atom interactions NBONDS: found 23076 intra-atom interactions NBONDS: found 23082 intra-atom interactions --------------- step= 2500 at 5.00000 ps -------------------------------- | E(kin)+E(total)=28812.612 E(kin)=6084.680 temperature=3015.215 | | Etotal =22727.932 grad(E)=123.657 E(BOND)=2625.205 E(ANGL)=6587.563 | | E(DIHE)=0.000 E(IMPR)=1919.035 E(VDW )=260.896 E(CDIH)=1772.794 | | E(NOE )=9163.291 E(PLAN)=399.148 | ------------------------------------------------------------------------------- NBONDS: found 23037 intra-atom interactions NBONDS: found 22943 intra-atom interactions NBONDS: found 22856 intra-atom interactions NBONDS: found 22699 intra-atom interactions NBONDS: found 22613 intra-atom interactions NBONDS: found 22602 intra-atom interactions NBONDS: found 22652 intra-atom interactions NBONDS: found 22678 intra-atom interactions --------------- step= 2600 at 5.20000 ps -------------------------------- | E(kin)+E(total)=28759.794 E(kin)=5983.543 temperature=2965.097 | | Etotal =22776.251 grad(E)=128.051 E(BOND)=2622.907 E(ANGL)=6781.175 | | E(DIHE)=0.000 E(IMPR)=1723.071 E(VDW )=255.157 E(CDIH)=1690.614 | | E(NOE )=9349.093 E(PLAN)=354.234 | ------------------------------------------------------------------------------- NBONDS: found 22709 intra-atom interactions NBONDS: found 22651 intra-atom interactions NBONDS: found 22578 intra-atom interactions NBONDS: found 22620 intra-atom interactions NBONDS: found 22650 intra-atom interactions NBONDS: found 22615 intra-atom interactions NBONDS: found 22543 intra-atom interactions --------------- step= 2700 at 5.40000 ps -------------------------------- | E(kin)+E(total)=28836.291 E(kin)=5855.550 temperature=2901.671 | | Etotal =22980.741 grad(E)=126.659 E(BOND)=2666.950 E(ANGL)=6640.042 | | E(DIHE)=0.000 E(IMPR)=2133.014 E(VDW )=247.712 E(CDIH)=1791.264 | | E(NOE )=9152.265 E(PLAN)=349.494 | ------------------------------------------------------------------------------- NBONDS: found 22545 intra-atom interactions NBONDS: found 22639 intra-atom interactions NBONDS: found 22833 intra-atom interactions NBONDS: found 22930 intra-atom interactions NBONDS: found 23048 intra-atom interactions NBONDS: found 23069 intra-atom interactions NBONDS: found 22990 intra-atom interactions --------------- step= 2800 at 5.60000 ps -------------------------------- | E(kin)+E(total)=28945.824 E(kin)=5942.820 temperature=2944.917 | | Etotal =23003.004 grad(E)=127.365 E(BOND)=2742.584 E(ANGL)=6816.609 | | E(DIHE)=0.000 E(IMPR)=1820.936 E(VDW )=262.460 E(CDIH)=1721.457 | | E(NOE )=9238.444 E(PLAN)=400.514 | ------------------------------------------------------------------------------- NBONDS: found 23134 intra-atom interactions NBONDS: found 23189 intra-atom interactions NBONDS: found 23321 intra-atom interactions NBONDS: found 23254 intra-atom interactions NBONDS: found 23253 intra-atom interactions NBONDS: found 23302 intra-atom interactions NBONDS: found 23311 intra-atom interactions --------------- step= 2900 at 5.80000 ps -------------------------------- | E(kin)+E(total)=28843.097 E(kin)=6204.261 temperature=3074.472 | | Etotal =22638.835 grad(E)=127.918 E(BOND)=2772.387 E(ANGL)=6350.436 | | E(DIHE)=0.000 E(IMPR)=1956.623 E(VDW )=260.136 E(CDIH)=1754.392 | | E(NOE )=9188.347 E(PLAN)=356.514 | ------------------------------------------------------------------------------- NBONDS: found 23386 intra-atom interactions NBONDS: found 23319 intra-atom interactions NBONDS: found 23333 intra-atom interactions NBONDS: found 23346 intra-atom interactions NBONDS: found 23335 intra-atom interactions NBONDS: found 23261 intra-atom interactions --------------- step= 3000 at 6.00000 ps -------------------------------- | E(kin)+E(total)=28817.990 E(kin)=6000.584 temperature=2973.541 | | Etotal =22817.407 grad(E)=126.984 E(BOND)=2755.837 E(ANGL)=6691.005 | | E(DIHE)=0.000 E(IMPR)=2001.144 E(VDW )=249.832 E(CDIH)=1621.340 | | E(NOE )=9067.666 E(PLAN)=430.583 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 0.00002 -0.00001 0.00002 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] : 0.00002 -0.00001 0.00002 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] : 0.00002 -0.00001 0.00002 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 23208 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=45989.969 E(kin)=6000.584 temperature=2973.541 | | Etotal =39989.386 grad(E)=316.251 E(BOND)=6889.592 E(ANGL)=16727.514 | | E(DIHE)=0.000 E(IMPR)=5002.859 E(VDW )=249.832 E(CDIH)=1621.340 | | E(NOE )=9067.666 E(PLAN)=430.583 | ------------------------------------------------------------------------------- NBONDS: found 23106 intra-atom interactions NBONDS: found 23068 intra-atom interactions NBONDS: found 23062 intra-atom interactions NBONDS: found 23140 intra-atom interactions NBONDS: found 23202 intra-atom interactions NBONDS: found 23214 intra-atom interactions NBONDS: found 23271 intra-atom interactions NBONDS: found 23350 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=37738.225 E(kin)=6707.141 temperature=3323.670 | | Etotal =31031.084 grad(E)=208.407 E(BOND)=3152.967 E(ANGL)=9579.988 | | E(DIHE)=0.000 E(IMPR)=2432.002 E(VDW )=253.836 E(CDIH)=1897.341 | | E(NOE )=13169.494 E(PLAN)=545.457 | ------------------------------------------------------------------------------- NBONDS: found 23473 intra-atom interactions NBONDS: found 23512 intra-atom interactions NBONDS: found 23663 intra-atom interactions NBONDS: found 23776 intra-atom interactions NBONDS: found 23872 intra-atom interactions NBONDS: found 23883 intra-atom interactions NBONDS: found 23803 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=36388.193 E(kin)=6234.178 temperature=3089.297 | | Etotal =30154.014 grad(E)=199.166 E(BOND)=2854.140 E(ANGL)=9006.314 | | E(DIHE)=0.000 E(IMPR)=2276.352 E(VDW )=260.281 E(CDIH)=1692.700 | | E(NOE )=13591.074 E(PLAN)=473.154 | ------------------------------------------------------------------------------- NBONDS: found 23751 intra-atom interactions NBONDS: found 23754 intra-atom interactions NBONDS: found 23801 intra-atom interactions NBONDS: found 23787 intra-atom interactions NBONDS: found 23731 intra-atom interactions NBONDS: found 23694 intra-atom interactions NBONDS: found 23598 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=36251.923 E(kin)=6214.851 temperature=3079.720 | | Etotal =30037.072 grad(E)=198.998 E(BOND)=2768.547 E(ANGL)=9183.550 | | E(DIHE)=0.000 E(IMPR)=2116.786 E(VDW )=255.525 E(CDIH)=1668.303 | | E(NOE )=13596.552 E(PLAN)=447.808 | ------------------------------------------------------------------------------- NBONDS: found 23616 intra-atom interactions NBONDS: found 23645 intra-atom interactions NBONDS: found 23796 intra-atom interactions NBONDS: found 23783 intra-atom interactions NBONDS: found 23913 intra-atom interactions NBONDS: found 24013 intra-atom interactions NBONDS: found 24212 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=36043.163 E(kin)=6130.791 temperature=3038.064 | | Etotal =29912.372 grad(E)=195.783 E(BOND)=2712.007 E(ANGL)=8613.418 | | E(DIHE)=0.000 E(IMPR)=2431.533 E(VDW )=267.495 E(CDIH)=1628.274 | | E(NOE )=13786.196 E(PLAN)=473.449 | ------------------------------------------------------------------------------- NBONDS: found 24328 intra-atom interactions NBONDS: found 24305 intra-atom interactions NBONDS: found 24382 intra-atom interactions NBONDS: found 24623 intra-atom interactions NBONDS: found 24710 intra-atom interactions NBONDS: found 24816 intra-atom interactions NBONDS: found 24947 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=36021.473 E(kin)=6071.536 temperature=3008.701 | | Etotal =29949.937 grad(E)=200.639 E(BOND)=2737.495 E(ANGL)=8461.004 | | E(DIHE)=0.000 E(IMPR)=2269.195 E(VDW )=277.614 E(CDIH)=1640.294 | | E(NOE )=14086.705 E(PLAN)=477.629 | ------------------------------------------------------------------------------- NBONDS: found 25160 intra-atom interactions NBONDS: found 25260 intra-atom interactions NBONDS: found 25383 intra-atom interactions NBONDS: found 25379 intra-atom interactions NBONDS: found 25356 intra-atom interactions NBONDS: found 25354 intra-atom interactions NBONDS: found 25494 intra-atom interactions NBONDS: found 25553 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=35835.502 E(kin)=6109.537 temperature=3027.532 | | Etotal =29725.965 grad(E)=196.693 E(BOND)=2669.274 E(ANGL)=8907.644 | | E(DIHE)=0.000 E(IMPR)=2166.090 E(VDW )=289.377 E(CDIH)=1665.729 | | E(NOE )=13573.170 E(PLAN)=454.681 | ------------------------------------------------------------------------------- NBONDS: found 25499 intra-atom interactions NBONDS: found 25446 intra-atom interactions NBONDS: found 25494 intra-atom interactions NBONDS: found 25548 intra-atom interactions NBONDS: found 25641 intra-atom interactions NBONDS: found 25776 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=35811.845 E(kin)=5859.289 temperature=2903.524 | | Etotal =29952.555 grad(E)=203.356 E(BOND)=3095.176 E(ANGL)=9112.812 | | E(DIHE)=0.000 E(IMPR)=1987.687 E(VDW )=293.615 E(CDIH)=1757.953 | | E(NOE )=13240.980 E(PLAN)=464.331 | ------------------------------------------------------------------------------- NBONDS: found 25866 intra-atom interactions NBONDS: found 25919 intra-atom interactions NBONDS: found 25936 intra-atom interactions NBONDS: found 25986 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00002 -0.00001 0.00002 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 19:21:24 created by user: COOR>ATOM 1 P GUA 1 14.209 3.014 7.103 1.00 0.00 A COOR>ATOM 2 O1P GUA 1 11.537 5.626 8.265 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 = 2.7055 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.7472 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9792 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9508 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0506 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2484 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9238 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.1573 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2003 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.9812 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.6151 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.5692 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.7063 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.4470 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2836 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1019 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.5560 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9356 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.5821 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.7850 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6503 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 15593 intra-atom interactions NBONDS: found 15648 intra-atom interactions NBONDS: found 15731 intra-atom interactions NBONDS: found 15791 intra-atom interactions NBONDS: found 15863 intra-atom interactions NBONDS: found 15942 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0002 ----------------------- | Etotal =109853.105 grad(E)=334.652 E(BOND)=15480.345 E(VDW )=13701.841 | | E(CDIH)=4308.323 E(NOE )=75735.493 E(PLAN)=627.102 | ------------------------------------------------------------------------------- NBONDS: found 15986 intra-atom interactions NBONDS: found 15974 intra-atom interactions NBONDS: found 15967 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =60454.939 grad(E)=183.883 E(BOND)=4727.856 E(VDW )=9861.836 | | E(CDIH)=2904.323 E(NOE )=42558.524 E(PLAN)=402.400 | ------------------------------------------------------------------------------- NBONDS: found 15909 intra-atom interactions NBONDS: found 15797 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =41883.578 grad(E)=111.067 E(BOND)=2065.274 E(VDW )=6861.175 | | E(CDIH)=2141.270 E(NOE )=30551.314 E(PLAN)=264.545 | ------------------------------------------------------------------------------- NBONDS: found 15666 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =33213.647 grad(E)=81.718 E(BOND)=1258.596 E(VDW )=5249.124 | | E(CDIH)=1897.444 E(NOE )=24543.362 E(PLAN)=265.120 | ------------------------------------------------------------------------------- NBONDS: found 15607 intra-atom interactions NBONDS: found 15533 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =27489.042 grad(E)=61.340 E(BOND)=1002.885 E(VDW )=4025.511 | | E(CDIH)=1903.589 E(NOE )=20279.274 E(PLAN)=277.783 | ------------------------------------------------------------------------------- NBONDS: found 15382 intra-atom interactions NBONDS: found 15470 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0000 ----------------------- | Etotal =24099.892 grad(E)=65.691 E(BOND)=915.939 E(VDW )=3426.608 | | E(CDIH)=1644.822 E(NOE )=17825.927 E(PLAN)=286.596 | ------------------------------------------------------------------------------- NBONDS: found 15401 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0000 ----------------------- | Etotal =22461.934 grad(E)=44.852 E(BOND)=723.024 E(VDW )=3079.591 | | E(CDIH)=1752.406 E(NOE )=16608.610 E(PLAN)=298.304 | ------------------------------------------------------------------------------- --------------- cycle= 80 ------ stepsize= 0.0000 ----------------------- | Etotal =22457.272 grad(E)=44.862 E(BOND)=723.588 E(VDW )=3078.705 | | E(CDIH)=1752.104 E(NOE )=16604.548 E(PLAN)=298.327 | ------------------------------------------------------------------------------- --------------- cycle= 90 ------ stepsize= 0.0000 ----------------------- | Etotal =22732.047 grad(E)=68.337 E(BOND)=723.612 E(VDW )=3078.671 | | E(CDIH)=2027.046 E(NOE )=16604.391 E(PLAN)=298.328 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =22457.095 grad(E)=44.863 E(BOND)=723.612 E(VDW )=3078.671 | | E(CDIH)=1752.093 E(NOE )=16604.391 E(PLAN)=298.328 | ------------------------------------------------------------------------------- %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 15358 intra-atom interactions NBONDS: found 15278 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =110850.529 grad(E)=410.772 E(BOND)=14880.428 E(ANGL)=65279.769 | | E(VDW )=4749.000 E(CDIH)=3120.556 E(NOE )=22248.948 E(PLAN)=571.828 | ------------------------------------------------------------------------------- NBONDS: found 15211 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =80752.936 grad(E)=195.491 E(BOND)=5458.936 E(ANGL)=38930.477 | | E(VDW )=5678.676 E(CDIH)=3657.037 E(NOE )=26456.824 E(PLAN)=570.986 | ------------------------------------------------------------------------------- NBONDS: found 15177 intra-atom interactions NBONDS: found 15139 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =67098.748 grad(E)=164.976 E(BOND)=4157.638 E(ANGL)=28498.356 | | E(VDW )=5451.797 E(CDIH)=3726.699 E(NOE )=24734.578 E(PLAN)=529.679 | ------------------------------------------------------------------------------- NBONDS: found 15071 intra-atom interactions NBONDS: found 14962 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =57398.567 grad(E)=129.730 E(BOND)=3087.468 E(ANGL)=21580.882 | | E(VDW )=5071.960 E(CDIH)=3678.399 E(NOE )=23541.423 E(PLAN)=438.435 | ------------------------------------------------------------------------------- NBONDS: found 14813 intra-atom interactions NBONDS: found 14620 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =51616.365 grad(E)=84.082 E(BOND)=2407.391 E(ANGL)=18633.032 | | E(VDW )=4684.376 E(CDIH)=3592.971 E(NOE )=21884.307 E(PLAN)=414.287 | ------------------------------------------------------------------------------- NBONDS: found 14471 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =47705.096 grad(E)=76.347 E(BOND)=2267.151 E(ANGL)=16632.873 | | E(VDW )=3922.724 E(CDIH)=3625.305 E(NOE )=20809.472 E(PLAN)=447.570 | ------------------------------------------------------------------------------- NBONDS: found 14345 intra-atom interactions NBONDS: found 14219 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =44012.410 grad(E)=75.464 E(BOND)=2185.048 E(ANGL)=15069.239 | | E(VDW )=3321.434 E(CDIH)=3501.441 E(NOE )=19488.741 E(PLAN)=446.507 | ------------------------------------------------------------------------------- NBONDS: found 14038 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =40870.365 grad(E)=67.737 E(BOND)=1798.209 E(ANGL)=13747.883 | | E(VDW )=3095.550 E(CDIH)=3431.575 E(NOE )=18375.589 E(PLAN)=421.558 | ------------------------------------------------------------------------------- NBONDS: found 13824 intra-atom interactions NBONDS: found 13637 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =38541.299 grad(E)=51.402 E(BOND)=1658.821 E(ANGL)=12784.717 | | E(VDW )=2871.451 E(CDIH)=3171.429 E(NOE )=17681.757 E(PLAN)=373.124 | ------------------------------------------------------------------------------- NBONDS: found 13443 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =36655.586 grad(E)=47.207 E(BOND)=1655.933 E(ANGL)=11960.505 | | E(VDW )=2668.692 E(CDIH)=2995.013 E(NOE )=17070.831 E(PLAN)=304.611 | ------------------------------------------------------------------------------- NBONDS: found 13342 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0001 ----------------------- | Etotal =34769.599 grad(E)=55.181 E(BOND)=1440.385 E(ANGL)=11335.269 | | E(VDW )=2310.407 E(CDIH)=2888.886 E(NOE )=16547.660 E(PLAN)=246.993 | ------------------------------------------------------------------------------- NBONDS: found 13222 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0001 ----------------------- | Etotal =33029.698 grad(E)=58.033 E(BOND)=1463.558 E(ANGL)=10906.869 | | E(VDW )=2086.262 E(CDIH)=2817.646 E(NOE )=15546.270 E(PLAN)=209.093 | ------------------------------------------------------------------------------- NBONDS: found 13091 intra-atom interactions NBONDS: found 13018 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0001 ----------------------- | Etotal =31505.512 grad(E)=50.934 E(BOND)=1335.252 E(ANGL)=10537.374 | | E(VDW )=2058.859 E(CDIH)=2748.547 E(NOE )=14622.819 E(PLAN)=202.661 | ------------------------------------------------------------------------------- NBONDS: found 12939 intra-atom interactions NBONDS: found 12879 intra-atom interactions NBONDS: found 12821 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0001 ----------------------- | Etotal =29738.033 grad(E)=59.138 E(BOND)=1262.560 E(ANGL)=9718.697 | | E(VDW )=2137.387 E(CDIH)=2711.769 E(NOE )=13696.700 E(PLAN)=210.920 | ------------------------------------------------------------------------------- NBONDS: found 12739 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =27778.891 grad(E)=51.191 E(BOND)=1140.582 E(ANGL)=8968.034 | | E(VDW )=2024.414 E(CDIH)=2644.853 E(NOE )=12801.187 E(PLAN)=199.822 | ------------------------------------------------------------------------------- NBONDS: found 12626 intra-atom interactions --------------- cycle= 160 ------ stepsize= 0.0001 ----------------------- | Etotal =25929.910 grad(E)=41.232 E(BOND)=1193.401 E(ANGL)=7338.814 | | E(VDW )=2011.010 E(CDIH)=2659.923 E(NOE )=12527.570 E(PLAN)=199.193 | ------------------------------------------------------------------------------- NBONDS: found 12546 intra-atom interactions --------------- cycle= 170 ------ stepsize= 0.0001 ----------------------- | Etotal =24149.735 grad(E)=53.299 E(BOND)=1088.954 E(ANGL)=6540.134 | | E(VDW )=1871.789 E(CDIH)=2650.964 E(NOE )=11801.741 E(PLAN)=196.155 | ------------------------------------------------------------------------------- NBONDS: found 12466 intra-atom interactions NBONDS: found 12347 intra-atom interactions --------------- cycle= 180 ------ stepsize= 0.0001 ----------------------- | Etotal =23022.327 grad(E)=39.965 E(BOND)=1049.099 E(ANGL)=6323.915 | | E(VDW )=1638.105 E(CDIH)=2637.482 E(NOE )=11185.264 E(PLAN)=188.461 | ------------------------------------------------------------------------------- --------------- cycle= 190 ------ stepsize= 0.0001 ----------------------- | Etotal =21901.882 grad(E)=46.099 E(BOND)=980.682 E(ANGL)=6106.658 | | E(VDW )=1475.921 E(CDIH)=2601.563 E(NOE )=10569.753 E(PLAN)=167.306 | ------------------------------------------------------------------------------- NBONDS: found 12146 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =20871.694 grad(E)=42.257 E(BOND)=874.574 E(ANGL)=5772.646 | | E(VDW )=1394.673 E(CDIH)=2602.249 E(NOE )=10084.881 E(PLAN)=142.671 | ------------------------------------------------------------------------------- NBONDS: found 12050 intra-atom interactions --------------- cycle= 210 ------ stepsize= 0.0001 ----------------------- | Etotal =20112.818 grad(E)=35.631 E(BOND)=793.659 E(ANGL)=5638.865 | | E(VDW )=1284.491 E(CDIH)=2583.093 E(NOE )=9677.676 E(PLAN)=135.034 | ------------------------------------------------------------------------------- NBONDS: found 11942 intra-atom interactions NBONDS: found 11877 intra-atom interactions --------------- cycle= 220 ------ stepsize= 0.0001 ----------------------- | Etotal =19345.238 grad(E)=36.022 E(BOND)=716.759 E(ANGL)=5610.118 | | E(VDW )=1205.764 E(CDIH)=2590.841 E(NOE )=9093.816 E(PLAN)=127.941 | ------------------------------------------------------------------------------- NBONDS: found 11830 intra-atom interactions --------------- cycle= 230 ------ stepsize= 0.0001 ----------------------- | Etotal =18600.714 grad(E)=34.360 E(BOND)=675.819 E(ANGL)=5451.831 | | E(VDW )=1197.629 E(CDIH)=2571.280 E(NOE )=8575.964 E(PLAN)=128.191 | ------------------------------------------------------------------------------- NBONDS: found 11792 intra-atom interactions --------------- cycle= 240 ------ stepsize= 0.0001 ----------------------- | Etotal =18035.016 grad(E)=28.781 E(BOND)=656.138 E(ANGL)=5204.687 | | E(VDW )=1193.430 E(CDIH)=2534.506 E(NOE )=8314.546 E(PLAN)=131.710 | ------------------------------------------------------------------------------- NBONDS: found 11737 intra-atom interactions --------------- cycle= 250 ------ stepsize= 0.0001 ----------------------- | Etotal =17548.702 grad(E)=28.098 E(BOND)=639.753 E(ANGL)=5058.129 | | E(VDW )=1166.017 E(CDIH)=2531.744 E(NOE )=8014.530 E(PLAN)=138.529 | ------------------------------------------------------------------------------- --------------- cycle= 260 ------ stepsize= 0.0001 ----------------------- | Etotal =17101.327 grad(E)=25.550 E(BOND)=628.667 E(ANGL)=4942.435 | | E(VDW )=1117.061 E(CDIH)=2517.567 E(NOE )=7753.446 E(PLAN)=142.151 | ------------------------------------------------------------------------------- NBONDS: found 11619 intra-atom interactions --------------- cycle= 270 ------ stepsize= 0.0001 ----------------------- | Etotal =16673.921 grad(E)=27.919 E(BOND)=638.531 E(ANGL)=4960.902 | | E(VDW )=1086.217 E(CDIH)=2459.622 E(NOE )=7392.257 E(PLAN)=136.392 | ------------------------------------------------------------------------------- NBONDS: found 11511 intra-atom interactions --------------- cycle= 280 ------ stepsize= 0.0001 ----------------------- | Etotal =16259.850 grad(E)=24.925 E(BOND)=629.912 E(ANGL)=4972.214 | | E(VDW )=1118.020 E(CDIH)=2419.698 E(NOE )=6999.095 E(PLAN)=120.911 | ------------------------------------------------------------------------------- --------------- cycle= 290 ------ stepsize= 0.0001 ----------------------- | Etotal =15847.240 grad(E)=24.610 E(BOND)=635.010 E(ANGL)=4864.153 | | E(VDW )=1110.694 E(CDIH)=2355.405 E(NOE )=6770.156 E(PLAN)=111.822 | ------------------------------------------------------------------------------- NBONDS: found 11467 intra-atom interactions --------------- cycle= 300 ------ stepsize= 0.0001 ----------------------- | Etotal =15463.933 grad(E)=23.853 E(BOND)=585.221 E(ANGL)=4754.206 | | E(VDW )=1089.341 E(CDIH)=2307.237 E(NOE )=6617.768 E(PLAN)=110.159 | ------------------------------------------------------------------------------- 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= 0.144271786E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : -0.00002 -0.00001 0.00002 velocity [A/ps] : -0.08466 0.01541 -0.03260 ang. mom. [amu A/ps] : 146485.34761 -96569.11530 76537.55275 kin. ener. [Kcal/mol] : 0.68503 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : -0.00002 -0.00001 0.00002 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 11432 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=20992.635 E(kin)=6071.623 temperature=3008.744 | | Etotal =14921.012 grad(E)=60.294 E(BOND)=58.522 E(ANGL)=475.421 | | E(DIHE)=0.000 E(IMPR)=4262.563 E(VDW )=1089.341 E(CDIH)=2307.237 | | E(NOE )=6617.768 E(PLAN)=110.159 | ------------------------------------------------------------------------------- NBONDS: found 11446 intra-atom interactions NBONDS: found 11453 intra-atom interactions NBONDS: found 11423 intra-atom interactions NBONDS: found 11413 intra-atom interactions NBONDS: found 11409 intra-atom interactions NBONDS: found 11387 intra-atom interactions NBONDS: found 11335 intra-atom interactions NBONDS: found 11285 intra-atom interactions NBONDS: found 11218 intra-atom interactions NBONDS: found 11197 intra-atom interactions NBONDS: found 11174 intra-atom interactions NBONDS: found 11160 intra-atom interactions NBONDS: found 11100 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=19021.980 E(kin)=6490.240 temperature=3216.187 | | Etotal =12531.740 grad(E)=71.038 E(BOND)=2543.812 E(ANGL)=4078.793 | | E(DIHE)=0.000 E(IMPR)=1442.283 E(VDW )=467.319 E(CDIH)=1031.140 | | E(NOE )=2909.122 E(PLAN)=59.272 | ------------------------------------------------------------------------------- NBONDS: found 11075 intra-atom interactions NBONDS: found 11060 intra-atom interactions NBONDS: found 11037 intra-atom interactions NBONDS: found 11014 intra-atom interactions NBONDS: found 10990 intra-atom interactions NBONDS: found 10950 intra-atom interactions NBONDS: found 10927 intra-atom interactions NBONDS: found 10979 intra-atom interactions NBONDS: found 10957 intra-atom interactions NBONDS: found 10939 intra-atom interactions NBONDS: found 10834 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=16339.622 E(kin)=6619.946 temperature=3280.461 | | Etotal =9719.677 grad(E)=64.990 E(BOND)=2205.738 E(ANGL)=2949.357 | | E(DIHE)=0.000 E(IMPR)=1019.564 E(VDW )=427.198 E(CDIH)=667.775 | | E(NOE )=2349.768 E(PLAN)=100.277 | ------------------------------------------------------------------------------- NBONDS: found 10805 intra-atom interactions NBONDS: found 10794 intra-atom interactions NBONDS: found 10750 intra-atom interactions NBONDS: found 10717 intra-atom interactions NBONDS: found 10699 intra-atom interactions NBONDS: found 10637 intra-atom interactions NBONDS: found 10650 intra-atom interactions NBONDS: found 10581 intra-atom interactions NBONDS: found 10540 intra-atom interactions NBONDS: found 10534 intra-atom interactions NBONDS: found 10445 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=14629.833 E(kin)=6494.852 temperature=3218.472 | | Etotal =8134.982 grad(E)=60.228 E(BOND)=1959.821 E(ANGL)=2748.508 | | E(DIHE)=0.000 E(IMPR)=925.506 E(VDW )=212.668 E(CDIH)=368.211 | | E(NOE )=1825.040 E(PLAN)=95.228 | ------------------------------------------------------------------------------- NBONDS: found 10352 intra-atom interactions NBONDS: found 10321 intra-atom interactions NBONDS: found 10263 intra-atom interactions NBONDS: found 10232 intra-atom interactions NBONDS: found 10231 intra-atom interactions NBONDS: found 10189 intra-atom interactions NBONDS: found 10146 intra-atom interactions NBONDS: found 10143 intra-atom interactions NBONDS: found 10144 intra-atom interactions NBONDS: found 10166 intra-atom interactions NBONDS: found 10196 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=14118.927 E(kin)=5808.706 temperature=2878.458 | | Etotal =8310.221 grad(E)=64.190 E(BOND)=2079.255 E(ANGL)=2686.871 | | E(DIHE)=0.000 E(IMPR)=846.738 E(VDW )=349.952 E(CDIH)=316.134 | | E(NOE )=1961.122 E(PLAN)=70.151 | ------------------------------------------------------------------------------- NBONDS: found 10162 intra-atom interactions NBONDS: found 10148 intra-atom interactions NBONDS: found 10107 intra-atom interactions NBONDS: found 10137 intra-atom interactions NBONDS: found 10143 intra-atom interactions NBONDS: found 10139 intra-atom interactions NBONDS: found 10121 intra-atom interactions NBONDS: found 10116 intra-atom interactions NBONDS: found 10151 intra-atom interactions NBONDS: found 10123 intra-atom interactions NBONDS: found 10095 intra-atom interactions NBONDS: found 10099 intra-atom interactions NBONDS: found 10117 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=13044.788 E(kin)=6459.662 temperature=3201.034 | | Etotal =6585.126 grad(E)=58.346 E(BOND)=1861.265 E(ANGL)=2236.355 | | E(DIHE)=0.000 E(IMPR)=755.138 E(VDW )=259.455 E(CDIH)=199.802 | | E(NOE )=1178.167 E(PLAN)=94.945 | ------------------------------------------------------------------------------- NBONDS: found 10199 intra-atom interactions NBONDS: found 10218 intra-atom interactions NBONDS: found 10190 intra-atom interactions NBONDS: found 10171 intra-atom interactions NBONDS: found 10147 intra-atom interactions NBONDS: found 10133 intra-atom interactions NBONDS: found 10138 intra-atom interactions NBONDS: found 10121 intra-atom interactions NBONDS: found 10111 intra-atom interactions NBONDS: found 10098 intra-atom interactions NBONDS: found 10069 intra-atom interactions NBONDS: found 10103 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=12795.068 E(kin)=5946.918 temperature=2946.948 | | Etotal =6848.150 grad(E)=59.429 E(BOND)=1815.394 E(ANGL)=2382.735 | | E(DIHE)=0.000 E(IMPR)=766.830 E(VDW )=273.966 E(CDIH)=172.022 | | E(NOE )=1326.379 E(PLAN)=110.824 | ------------------------------------------------------------------------------- NBONDS: found 10105 intra-atom interactions NBONDS: found 10126 intra-atom interactions NBONDS: found 10099 intra-atom interactions NBONDS: found 10096 intra-atom interactions NBONDS: found 10088 intra-atom interactions NBONDS: found 10037 intra-atom interactions NBONDS: found 10026 intra-atom interactions NBONDS: found 9950 intra-atom interactions NBONDS: found 9893 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=12530.495 E(kin)=6020.353 temperature=2983.338 | | Etotal =6510.143 grad(E)=59.751 E(BOND)=1876.134 E(ANGL)=2373.190 | | E(DIHE)=0.000 E(IMPR)=695.693 E(VDW )=198.038 E(CDIH)=155.772 | | E(NOE )=1137.504 E(PLAN)=73.812 | ------------------------------------------------------------------------------- NBONDS: found 9876 intra-atom interactions NBONDS: found 9825 intra-atom interactions NBONDS: found 9754 intra-atom interactions NBONDS: found 9711 intra-atom interactions NBONDS: found 9693 intra-atom interactions CENMAS: Information about center of free masses position [A] : -0.00002 -0.00001 0.00002 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] : -0.00002 -0.00001 0.00002 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] : -0.00002 -0.00001 0.00002 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 9652 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=16540.365 E(kin)=6222.519 temperature=3083.519 | | Etotal =10317.847 grad(E)=108.664 E(BOND)=3420.366 E(ANGL)=4186.607 | | E(DIHE)=0.000 E(IMPR)=1255.561 E(VDW )=176.416 E(CDIH)=192.214 | | E(NOE )=1025.540 E(PLAN)=61.143 | ------------------------------------------------------------------------------- NBONDS: found 9603 intra-atom interactions NBONDS: found 9606 intra-atom interactions NBONDS: found 9594 intra-atom interactions NBONDS: found 9557 intra-atom interactions NBONDS: found 9526 intra-atom interactions NBONDS: found 9484 intra-atom interactions NBONDS: found 9457 intra-atom interactions NBONDS: found 9427 intra-atom interactions NBONDS: found 9476 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=12908.312 E(kin)=6298.369 temperature=3121.107 | | Etotal =6609.942 grad(E)=83.901 E(BOND)=1953.705 E(ANGL)=2361.581 | | E(DIHE)=0.000 E(IMPR)=822.656 E(VDW )=309.223 E(CDIH)=272.215 | | E(NOE )=827.620 E(PLAN)=62.942 | ------------------------------------------------------------------------------- NBONDS: found 9482 intra-atom interactions NBONDS: found 9495 intra-atom interactions NBONDS: found 9456 intra-atom interactions NBONDS: found 9520 intra-atom interactions NBONDS: found 9515 intra-atom interactions NBONDS: found 9550 intra-atom interactions NBONDS: found 9533 intra-atom interactions NBONDS: found 9555 intra-atom interactions NBONDS: found 9559 intra-atom interactions NBONDS: found 9617 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=12515.078 E(kin)=6087.660 temperature=3016.691 | | Etotal =6427.418 grad(E)=82.050 E(BOND)=1835.989 E(ANGL)=2330.665 | | E(DIHE)=0.000 E(IMPR)=843.927 E(VDW )=251.045 E(CDIH)=231.370 | | E(NOE )=912.673 E(PLAN)=21.748 | ------------------------------------------------------------------------------- NBONDS: found 9679 intra-atom interactions NBONDS: found 9699 intra-atom interactions NBONDS: found 9724 intra-atom interactions NBONDS: found 9748 intra-atom interactions NBONDS: found 9777 intra-atom interactions NBONDS: found 9803 intra-atom interactions NBONDS: found 9840 intra-atom interactions NBONDS: found 9801 intra-atom interactions NBONDS: found 9805 intra-atom interactions NBONDS: found 9770 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=12669.302 E(kin)=6202.540 temperature=3073.619 | | Etotal =6466.762 grad(E)=82.697 E(BOND)=1687.288 E(ANGL)=2380.525 | | E(DIHE)=0.000 E(IMPR)=877.395 E(VDW )=291.236 E(CDIH)=185.616 | | E(NOE )=987.623 E(PLAN)=57.079 | ------------------------------------------------------------------------------- NBONDS: found 9748 intra-atom interactions NBONDS: found 9736 intra-atom interactions NBONDS: found 9735 intra-atom interactions NBONDS: found 9725 intra-atom interactions NBONDS: found 9726 intra-atom interactions NBONDS: found 9699 intra-atom interactions NBONDS: found 9650 intra-atom interactions NBONDS: found 9683 intra-atom interactions NBONDS: found 9741 intra-atom interactions NBONDS: found 9752 intra-atom interactions NBONDS: found 9813 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=12537.171 E(kin)=5917.410 temperature=2932.325 | | Etotal =6619.761 grad(E)=85.173 E(BOND)=1833.547 E(ANGL)=2361.060 | | E(DIHE)=0.000 E(IMPR)=870.754 E(VDW )=290.731 E(CDIH)=177.747 | | E(NOE )=1041.372 E(PLAN)=44.550 | ------------------------------------------------------------------------------- NBONDS: found 9791 intra-atom interactions NBONDS: found 9820 intra-atom interactions NBONDS: found 9859 intra-atom interactions NBONDS: found 9843 intra-atom interactions NBONDS: found 9879 intra-atom interactions NBONDS: found 9885 intra-atom interactions NBONDS: found 9916 intra-atom interactions NBONDS: found 9935 intra-atom interactions NBONDS: found 9973 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=12614.930 E(kin)=5985.615 temperature=2966.123 | | Etotal =6629.315 grad(E)=83.157 E(BOND)=1797.269 E(ANGL)=2524.656 | | E(DIHE)=0.000 E(IMPR)=903.498 E(VDW )=264.929 E(CDIH)=184.863 | | E(NOE )=897.242 E(PLAN)=56.860 | ------------------------------------------------------------------------------- NBONDS: found 9985 intra-atom interactions NBONDS: found 10044 intra-atom interactions NBONDS: found 10077 intra-atom interactions NBONDS: found 10103 intra-atom interactions NBONDS: found 10107 intra-atom interactions NBONDS: found 10116 intra-atom interactions NBONDS: found 10118 intra-atom interactions NBONDS: found 10114 intra-atom interactions NBONDS: found 10074 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=12666.869 E(kin)=6033.077 temperature=2989.643 | | Etotal =6633.792 grad(E)=83.099 E(BOND)=1911.947 E(ANGL)=2275.275 | | E(DIHE)=0.000 E(IMPR)=856.896 E(VDW )=288.750 E(CDIH)=166.726 | | E(NOE )=1084.632 E(PLAN)=49.565