X-PLOR: V3.840 user: on: Alpha/OSF at: 16-Aug-96 16:21:22 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=18026.5679626465 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 16:19:36 created by user: COOR>ATOM 1 P GUA 1 13.124 3.955 8.029 1.00 0.00 A COOR>ATOM 2 O1P GUA 1 12.913 3.265 8.771 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 = 2.5617 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.7584 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2344 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2315 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.4180 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.3579 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6037 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.3773 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.3588 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6696 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.0548 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.3496 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6764 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.2579 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.3196 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.3349 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9602 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8247 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.8031 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2692 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6770 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 14772 intra-atom interactions NBONDS: found 14850 intra-atom interactions NBONDS: found 14987 intra-atom interactions NBONDS: found 15090 intra-atom interactions NBONDS: found 15302 intra-atom interactions NBONDS: found 15529 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =123705.006 grad(E)=368.414 E(BOND)=17474.810 E(VDW )=11569.612 | | E(CDIH)=4581.404 E(NOE )=89381.657 E(PLAN)=697.523 | ------------------------------------------------------------------------------- NBONDS: found 15586 intra-atom interactions NBONDS: found 15697 intra-atom interactions NBONDS: found 15752 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0002 ----------------------- | Etotal =69840.988 grad(E)=163.004 E(BOND)=4208.238 E(VDW )=9151.921 | | E(CDIH)=3748.035 E(NOE )=52259.148 E(PLAN)=473.646 | ------------------------------------------------------------------------------- NBONDS: found 15810 intra-atom interactions NBONDS: found 15838 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0002 ----------------------- | Etotal =49730.274 grad(E)=170.254 E(BOND)=3219.781 E(VDW )=6445.793 | | E(CDIH)=3229.105 E(NOE )=36534.796 E(PLAN)=300.798 | ------------------------------------------------------------------------------- NBONDS: found 15830 intra-atom interactions NBONDS: found 15810 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =38823.955 grad(E)=104.524 E(BOND)=2042.586 E(VDW )=4753.406 | | E(CDIH)=2593.316 E(NOE )=29151.308 E(PLAN)=283.339 | ------------------------------------------------------------------------------- NBONDS: found 15831 intra-atom interactions NBONDS: found 15748 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =31760.385 grad(E)=68.897 E(BOND)=1340.066 E(VDW )=3846.213 | | E(CDIH)=2391.552 E(NOE )=23908.555 E(PLAN)=273.998 | ------------------------------------------------------------------------------- NBONDS: found 15636 intra-atom interactions NBONDS: found 15543 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0000 ----------------------- | Etotal =27854.320 grad(E)=65.837 E(BOND)=1095.394 E(VDW )=3094.348 | | E(CDIH)=2168.947 E(NOE )=21192.018 E(PLAN)=303.612 | ------------------------------------------------------------------------------- NBONDS: found 15397 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0000 ----------------------- | Etotal =24726.159 grad(E)=64.975 E(BOND)=986.263 E(VDW )=2735.837 | | E(CDIH)=1837.234 E(NOE )=18865.343 E(PLAN)=301.483 | ------------------------------------------------------------------------------- NBONDS: found 15087 intra-atom interactions NBONDS: found 15284 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0000 ----------------------- | Etotal =22059.677 grad(E)=56.584 E(BOND)=718.488 E(VDW )=2238.906 | | E(CDIH)=1806.176 E(NOE )=17028.284 E(PLAN)=267.823 | ------------------------------------------------------------------------------- NBONDS: found 15222 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0000 ----------------------- | Etotal =21581.060 grad(E)=62.878 E(BOND)=740.582 E(VDW )=2171.919 | | E(CDIH)=1957.506 E(NOE )=16454.618 E(PLAN)=256.434 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =21409.437 grad(E)=46.413 E(BOND)=739.849 E(VDW )=2171.987 | | E(CDIH)=1785.003 E(NOE )=16456.125 E(PLAN)=256.473 | ------------------------------------------------------------------------------- --------------- cycle= 110 ------ stepsize= 0.0000 ----------------------- | Etotal =21409.338 grad(E)=46.414 E(BOND)=739.901 E(VDW )=2171.982 | | E(CDIH)=1784.967 E(NOE )=16456.017 E(PLAN)=256.470 | ------------------------------------------------------------------------------- --------------- cycle= 120 ------ stepsize= 0.0000 ----------------------- | Etotal =21409.329 grad(E)=46.414 E(BOND)=739.906 E(VDW )=2171.982 | | E(CDIH)=1784.964 E(NOE )=16456.007 E(PLAN)=256.470 | ------------------------------------------------------------------------------- --------------- cycle= 130 ------ stepsize= 0.0000 ----------------------- | Etotal =21582.184 grad(E)=62.913 E(BOND)=739.907 E(VDW )=2171.982 | | E(CDIH)=1957.820 E(NOE )=16456.006 E(PLAN)=256.470 | ------------------------------------------------------------------------------- %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 15218 intra-atom interactions NBONDS: found 15181 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =127467.072 grad(E)=393.225 E(BOND)=15773.130 E(ANGL)=81260.137 | | E(VDW )=3812.228 E(CDIH)=3706.754 E(NOE )=22417.959 E(PLAN)=496.863 | ------------------------------------------------------------------------------- NBONDS: found 15142 intra-atom interactions NBONDS: found 15087 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =84934.015 grad(E)=203.405 E(BOND)=5865.880 E(ANGL)=41799.970 | | E(VDW )=4673.437 E(CDIH)=4650.501 E(NOE )=27442.297 E(PLAN)=501.930 | ------------------------------------------------------------------------------- NBONDS: found 15080 intra-atom interactions NBONDS: found 15016 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =72123.068 grad(E)=140.541 E(BOND)=3630.447 E(ANGL)=31629.093 | | E(VDW )=4617.260 E(CDIH)=4764.967 E(NOE )=26967.926 E(PLAN)=513.375 | ------------------------------------------------------------------------------- NBONDS: found 14997 intra-atom interactions NBONDS: found 14915 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =65445.820 grad(E)=93.283 E(BOND)=3195.817 E(ANGL)=26679.469 | | E(VDW )=4371.509 E(CDIH)=4700.071 E(NOE )=25980.986 E(PLAN)=517.967 | ------------------------------------------------------------------------------- NBONDS: found 14830 intra-atom interactions NBONDS: found 14706 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =59088.392 grad(E)=103.889 E(BOND)=2793.335 E(ANGL)=22764.357 | | E(VDW )=3545.935 E(CDIH)=4466.571 E(NOE )=24962.964 E(PLAN)=555.231 | ------------------------------------------------------------------------------- NBONDS: found 14598 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =55111.464 grad(E)=87.669 E(BOND)=2628.522 E(ANGL)=21221.881 | | E(VDW )=3134.454 E(CDIH)=4471.989 E(NOE )=23073.574 E(PLAN)=581.044 | ------------------------------------------------------------------------------- NBONDS: found 14513 intra-atom interactions NBONDS: found 14454 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =50210.211 grad(E)=67.025 E(BOND)=2309.473 E(ANGL)=18055.919 | | E(VDW )=2871.813 E(CDIH)=4369.785 E(NOE )=22052.790 E(PLAN)=550.432 | ------------------------------------------------------------------------------- NBONDS: found 14375 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =47444.530 grad(E)=62.473 E(BOND)=1987.291 E(ANGL)=16957.637 | | E(VDW )=2529.075 E(CDIH)=4284.113 E(NOE )=21142.694 E(PLAN)=543.720 | ------------------------------------------------------------------------------- NBONDS: found 14311 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =45657.463 grad(E)=46.495 E(BOND)=1846.027 E(ANGL)=15952.790 | | E(VDW )=2338.919 E(CDIH)=4247.814 E(NOE )=20721.792 E(PLAN)=550.122 | ------------------------------------------------------------------------------- NBONDS: found 14227 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =43890.014 grad(E)=57.029 E(BOND)=1821.681 E(ANGL)=15032.531 | | E(VDW )=2100.553 E(CDIH)=4265.499 E(NOE )=20101.129 E(PLAN)=568.622 | ------------------------------------------------------------------------------- NBONDS: found 14144 intra-atom interactions NBONDS: found 14046 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0001 ----------------------- | Etotal =42391.170 grad(E)=50.512 E(BOND)=1624.060 E(ANGL)=14168.144 | | E(VDW )=2012.939 E(CDIH)=4228.315 E(NOE )=19793.517 E(PLAN)=564.194 | ------------------------------------------------------------------------------- NBONDS: found 13931 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0001 ----------------------- | Etotal =40959.518 grad(E)=43.168 E(BOND)=1379.026 E(ANGL)=13528.974 | | E(VDW )=1915.832 E(CDIH)=4143.633 E(NOE )=19452.696 E(PLAN)=539.358 | ------------------------------------------------------------------------------- NBONDS: found 13767 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0001 ----------------------- | Etotal =39320.609 grad(E)=47.272 E(BOND)=1398.512 E(ANGL)=12471.836 | | E(VDW )=1642.365 E(CDIH)=4135.426 E(NOE )=19172.013 E(PLAN)=500.458 | ------------------------------------------------------------------------------- NBONDS: found 13601 intra-atom interactions NBONDS: found 13539 intra-atom interactions NBONDS: found 13507 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0001 ----------------------- | Etotal =37157.668 grad(E)=52.588 E(BOND)=1447.564 E(ANGL)=9934.605 | | E(VDW )=1474.324 E(CDIH)=4164.855 E(NOE )=19665.976 E(PLAN)=470.344 | ------------------------------------------------------------------------------- NBONDS: found 13476 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =35685.956 grad(E)=36.040 E(BOND)=1280.944 E(ANGL)=8792.727 | | E(VDW )=1407.517 E(CDIH)=4176.167 E(NOE )=19556.875 E(PLAN)=471.726 | ------------------------------------------------------------------------------- --------------- cycle= 160 ------ stepsize= 0.0001 ----------------------- | Etotal =34790.381 grad(E)=37.104 E(BOND)=1150.546 E(ANGL)=8608.686 | | E(VDW )=1381.486 E(CDIH)=4169.541 E(NOE )=19000.732 E(PLAN)=479.390 | ------------------------------------------------------------------------------- NBONDS: found 13433 intra-atom interactions --------------- cycle= 170 ------ stepsize= 0.0001 ----------------------- | Etotal =34138.092 grad(E)=28.507 E(BOND)=1210.301 E(ANGL)=8329.461 | | E(VDW )=1317.321 E(CDIH)=4150.695 E(NOE )=18644.857 E(PLAN)=485.457 | ------------------------------------------------------------------------------- NBONDS: found 13383 intra-atom interactions NBONDS: found 13274 intra-atom interactions --------------- cycle= 180 ------ stepsize= 0.0001 ----------------------- | Etotal =33541.080 grad(E)=36.906 E(BOND)=1171.456 E(ANGL)=8419.783 | | E(VDW )=1203.162 E(CDIH)=4117.104 E(NOE )=18133.931 E(PLAN)=495.644 | ------------------------------------------------------------------------------- NBONDS: found 13156 intra-atom interactions --------------- cycle= 190 ------ stepsize= 0.0001 ----------------------- | Etotal =32948.505 grad(E)=30.757 E(BOND)=1172.408 E(ANGL)=8369.361 | | E(VDW )=1025.224 E(CDIH)=4092.756 E(NOE )=17782.737 E(PLAN)=506.019 | ------------------------------------------------------------------------------- NBONDS: found 13048 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =32380.986 grad(E)=26.576 E(BOND)=1123.134 E(ANGL)=8205.637 | | E(VDW )=874.410 E(CDIH)=4082.502 E(NOE )=17572.516 E(PLAN)=522.787 | ------------------------------------------------------------------------------- NBONDS: found 12977 intra-atom interactions --------------- cycle= 210 ------ stepsize= 0.0001 ----------------------- | Etotal =32014.008 grad(E)=28.028 E(BOND)=1119.612 E(ANGL)=8111.189 | | E(VDW )=807.087 E(CDIH)=4068.782 E(NOE )=17382.354 E(PLAN)=524.983 | ------------------------------------------------------------------------------- --------------- cycle= 220 ------ stepsize= 0.0001 ----------------------- | Etotal =31596.856 grad(E)=24.426 E(BOND)=1048.401 E(ANGL)=7913.998 | | E(VDW )=755.488 E(CDIH)=4055.912 E(NOE )=17314.778 E(PLAN)=508.279 | ------------------------------------------------------------------------------- NBONDS: found 12928 intra-atom interactions --------------- cycle= 230 ------ stepsize= 0.0001 ----------------------- | Etotal =31296.193 grad(E)=20.961 E(BOND)=1015.251 E(ANGL)=7804.133 | | E(VDW )=707.348 E(CDIH)=4058.610 E(NOE )=17215.974 E(PLAN)=494.876 | ------------------------------------------------------------------------------- NBONDS: found 12832 intra-atom interactions --------------- cycle= 240 ------ stepsize= 0.0001 ----------------------- | Etotal =31005.837 grad(E)=23.878 E(BOND)=1059.923 E(ANGL)=7709.257 | | E(VDW )=653.794 E(CDIH)=4009.322 E(NOE )=17095.740 E(PLAN)=477.802 | ------------------------------------------------------------------------------- NBONDS: found 12692 intra-atom interactions --------------- cycle= 250 ------ stepsize= 0.0001 ----------------------- | Etotal =30649.676 grad(E)=24.307 E(BOND)=1045.178 E(ANGL)=7640.909 | | E(VDW )=631.971 E(CDIH)=3850.343 E(NOE )=17018.501 E(PLAN)=462.773 | ------------------------------------------------------------------------------- NBONDS: found 12625 intra-atom interactions --------------- cycle= 260 ------ stepsize= 0.0001 ----------------------- | Etotal =30242.198 grad(E)=29.117 E(BOND)=1005.503 E(ANGL)=7680.606 | | E(VDW )=593.719 E(CDIH)=3716.645 E(NOE )=16805.201 E(PLAN)=440.525 | ------------------------------------------------------------------------------- NBONDS: found 12577 intra-atom interactions --------------- cycle= 270 ------ stepsize= 0.0001 ----------------------- | Etotal =29908.611 grad(E)=24.624 E(BOND)=1030.395 E(ANGL)=7666.002 | | E(VDW )=556.462 E(CDIH)=3600.335 E(NOE )=16651.713 E(PLAN)=403.704 | ------------------------------------------------------------------------------- --------------- cycle= 280 ------ stepsize= 0.0001 ----------------------- | Etotal =29614.013 grad(E)=23.821 E(BOND)=1012.365 E(ANGL)=7622.032 | | E(VDW )=562.928 E(CDIH)=3515.477 E(NOE )=16518.231 E(PLAN)=382.980 | ------------------------------------------------------------------------------- NBONDS: found 12547 intra-atom interactions --------------- cycle= 290 ------ stepsize= 0.0001 ----------------------- | Etotal =29282.526 grad(E)=21.073 E(BOND)=966.771 E(ANGL)=7471.085 | | E(VDW )=545.118 E(CDIH)=3471.381 E(NOE )=16441.406 E(PLAN)=386.765 | ------------------------------------------------------------------------------- --------------- cycle= 300 ------ stepsize= 0.0001 ----------------------- | Etotal =29038.382 grad(E)=20.573 E(BOND)=978.844 E(ANGL)=7374.017 | | E(VDW )=546.140 E(CDIH)=3448.742 E(NOE )=16292.409 E(PLAN)=398.230 | ------------------------------------------------------------------------------- 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= 0.181384201E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 0.00001 0.00001 0.00001 velocity [A/ps] : 0.12281 -0.08549 0.18740 ang. mom. [amu A/ps] : 251910.42655-193849.88548 -73699.97791 kin. ener. [Kcal/mol] : 4.65274 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00001 0.00001 0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 CODIMP: improper type-based parameters retrieved NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 728 exclusions and 0 interactions(1-4) NBONDS: found 12518 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=37875.845 E(kin)=5862.866 temperature=2905.296 | | Etotal =32012.979 grad(E)=80.370 E(BOND)=97.884 E(ANGL)=737.402 | | E(DIHE)=0.000 E(IMPR)=10492.172 E(VDW )=546.140 E(CDIH)=3448.742 | | E(NOE )=16292.409 E(PLAN)=398.230 | ------------------------------------------------------------------------------- NBONDS: found 12504 intra-atom interactions NBONDS: found 12451 intra-atom interactions NBONDS: found 12449 intra-atom interactions NBONDS: found 12444 intra-atom interactions NBONDS: found 12438 intra-atom interactions NBONDS: found 12377 intra-atom interactions NBONDS: found 12334 intra-atom interactions NBONDS: found 12320 intra-atom interactions NBONDS: found 12299 intra-atom interactions NBONDS: found 12305 intra-atom interactions NBONDS: found 12299 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=34805.178 E(kin)=7406.737 temperature=3670.349 | | Etotal =27398.441 grad(E)=71.478 E(BOND)=3278.166 E(ANGL)=5714.868 | | E(DIHE)=0.000 E(IMPR)=6448.878 E(VDW )=464.032 E(CDIH)=1802.540 | | E(NOE )=9506.949 E(PLAN)=183.007 | ------------------------------------------------------------------------------- NBONDS: found 12292 intra-atom interactions NBONDS: found 12313 intra-atom interactions NBONDS: found 12294 intra-atom interactions NBONDS: found 12260 intra-atom interactions NBONDS: found 12180 intra-atom interactions NBONDS: found 12115 intra-atom interactions NBONDS: found 12062 intra-atom interactions NBONDS: found 12021 intra-atom interactions NBONDS: found 11995 intra-atom interactions NBONDS: found 11934 intra-atom interactions NBONDS: found 11872 intra-atom interactions NBONDS: found 11850 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=31492.806 E(kin)=6987.539 temperature=3462.619 | | Etotal =24505.266 grad(E)=70.683 E(BOND)=2772.660 E(ANGL)=5112.279 | | E(DIHE)=0.000 E(IMPR)=5986.072 E(VDW )=541.810 E(CDIH)=1697.738 | | E(NOE )=8167.198 E(PLAN)=227.510 | ------------------------------------------------------------------------------- NBONDS: found 11805 intra-atom interactions NBONDS: found 11800 intra-atom interactions NBONDS: found 11770 intra-atom interactions NBONDS: found 11763 intra-atom interactions NBONDS: found 11733 intra-atom interactions NBONDS: found 11686 intra-atom interactions NBONDS: found 11663 intra-atom interactions NBONDS: found 11666 intra-atom interactions NBONDS: found 11651 intra-atom interactions NBONDS: found 11632 intra-atom interactions NBONDS: found 11602 intra-atom interactions NBONDS: found 11560 intra-atom interactions NBONDS: found 11488 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=29017.076 E(kin)=6308.833 temperature=3126.292 | | Etotal =22708.243 grad(E)=68.530 E(BOND)=2713.960 E(ANGL)=5121.894 | | E(DIHE)=0.000 E(IMPR)=5255.160 E(VDW )=383.266 E(CDIH)=1476.658 | | E(NOE )=7592.738 E(PLAN)=164.567 | ------------------------------------------------------------------------------- NBONDS: found 11470 intra-atom interactions NBONDS: found 11506 intra-atom interactions NBONDS: found 11522 intra-atom interactions NBONDS: found 11555 intra-atom interactions NBONDS: found 11566 intra-atom interactions NBONDS: found 11572 intra-atom interactions NBONDS: found 11560 intra-atom interactions NBONDS: found 11539 intra-atom interactions NBONDS: found 11547 intra-atom interactions NBONDS: found 11573 intra-atom interactions NBONDS: found 11582 intra-atom interactions NBONDS: found 11598 intra-atom interactions NBONDS: found 11619 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=27092.479 E(kin)=6587.434 temperature=3264.350 | | Etotal =20505.046 grad(E)=67.276 E(BOND)=2864.782 E(ANGL)=4572.074 | | E(DIHE)=0.000 E(IMPR)=4731.877 E(VDW )=452.159 E(CDIH)=1119.717 | | E(NOE )=6582.150 E(PLAN)=182.286 | ------------------------------------------------------------------------------- NBONDS: found 11623 intra-atom interactions NBONDS: found 11627 intra-atom interactions NBONDS: found 11617 intra-atom interactions NBONDS: found 11656 intra-atom interactions NBONDS: found 11699 intra-atom interactions NBONDS: found 11704 intra-atom interactions NBONDS: found 11725 intra-atom interactions NBONDS: found 11702 intra-atom interactions NBONDS: found 11729 intra-atom interactions NBONDS: found 11771 intra-atom interactions NBONDS: found 11816 intra-atom interactions NBONDS: found 11855 intra-atom interactions NBONDS: found 11876 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=25896.981 E(kin)=6586.964 temperature=3264.117 | | Etotal =19310.017 grad(E)=67.444 E(BOND)=2488.858 E(ANGL)=4511.545 | | E(DIHE)=0.000 E(IMPR)=4550.609 E(VDW )=439.528 E(CDIH)=1198.325 | | E(NOE )=5980.853 E(PLAN)=140.298 | ------------------------------------------------------------------------------- NBONDS: found 11922 intra-atom interactions NBONDS: found 11940 intra-atom interactions NBONDS: found 11968 intra-atom interactions NBONDS: found 11989 intra-atom interactions NBONDS: found 12026 intra-atom interactions NBONDS: found 12044 intra-atom interactions NBONDS: found 12058 intra-atom interactions NBONDS: found 12038 intra-atom interactions NBONDS: found 12106 intra-atom interactions NBONDS: found 12109 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=25412.808 E(kin)=6215.743 temperature=3080.162 | | Etotal =19197.065 grad(E)=68.962 E(BOND)=2784.275 E(ANGL)=4628.539 | | E(DIHE)=0.000 E(IMPR)=4446.898 E(VDW )=342.323 E(CDIH)=1315.042 | | E(NOE )=5558.868 E(PLAN)=121.118 | ------------------------------------------------------------------------------- NBONDS: found 12159 intra-atom interactions NBONDS: found 12222 intra-atom interactions NBONDS: found 12244 intra-atom interactions NBONDS: found 12236 intra-atom interactions NBONDS: found 12247 intra-atom interactions NBONDS: found 12273 intra-atom interactions NBONDS: found 12302 intra-atom interactions NBONDS: found 12292 intra-atom interactions NBONDS: found 12275 intra-atom interactions NBONDS: found 12212 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=24832.873 E(kin)=6282.106 temperature=3113.047 | | Etotal =18550.767 grad(E)=69.327 E(BOND)=2407.635 E(ANGL)=4147.290 | | E(DIHE)=0.000 E(IMPR)=4492.289 E(VDW )=279.435 E(CDIH)=1299.231 | | E(NOE )=5755.717 E(PLAN)=169.170 | ------------------------------------------------------------------------------- NBONDS: found 12194 intra-atom interactions NBONDS: found 12185 intra-atom interactions NBONDS: found 12129 intra-atom interactions NBONDS: found 12075 intra-atom interactions NBONDS: found 12000 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00001 0.00001 0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> constraints inter (all) (all) weights * 0.2 dihe 0.1 impr 0.1 vdw 20 end end SELRPN: 677 atoms have been selected out of 677 SELRPN: 677 atoms have been selected out of 677 X-PLOR> dynamics verlet DYNAmics> nstep=$nstep1 time=$high_timestep iasvel=current firstt=$init_t DYNAmics> tcoup=true tbath=$init_t nprint=100 iprfrq=0 DYNAmics> end DYNAMC: number of degrees of freedom= 2031 ASSVEL: current velocities taken. CENMAS: Information about center of free masses position [A] : 0.00001 0.00001 0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00001 0.00001 0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 728 exclusions and 0 interactions(1-4) NBONDS: found 11976 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=35596.916 E(kin)=6421.008 temperature=3181.879 | | Etotal =29175.908 grad(E)=118.353 E(BOND)=4775.281 E(ANGL)=8253.638 | | E(DIHE)=0.000 E(IMPR)=9059.776 E(VDW )=229.994 E(CDIH)=1249.569 | | E(NOE )=5521.782 E(PLAN)=85.867 | ------------------------------------------------------------------------------- NBONDS: found 11993 intra-atom interactions NBONDS: found 12013 intra-atom interactions NBONDS: found 12019 intra-atom interactions NBONDS: found 12048 intra-atom interactions NBONDS: found 12095 intra-atom interactions NBONDS: found 12064 intra-atom interactions NBONDS: found 12078 intra-atom interactions NBONDS: found 12068 intra-atom interactions NBONDS: found 12099 intra-atom interactions NBONDS: found 12135 intra-atom interactions NBONDS: found 12186 intra-atom interactions NBONDS: found 12238 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=32166.945 E(kin)=6596.686 temperature=3268.935 | | Etotal =25570.258 grad(E)=97.101 E(BOND)=2916.855 E(ANGL)=5970.242 | | E(DIHE)=0.000 E(IMPR)=7731.879 E(VDW )=473.907 E(CDIH)=1583.366 | | E(NOE )=6658.723 E(PLAN)=235.287 | ------------------------------------------------------------------------------- NBONDS: found 12262 intra-atom interactions NBONDS: found 12283 intra-atom interactions NBONDS: found 12298 intra-atom interactions NBONDS: found 12308 intra-atom interactions NBONDS: found 12290 intra-atom interactions NBONDS: found 12327 intra-atom interactions NBONDS: found 12339 intra-atom interactions NBONDS: found 12342 intra-atom interactions NBONDS: found 12395 intra-atom interactions NBONDS: found 12376 intra-atom interactions NBONDS: found 12398 intra-atom interactions NBONDS: found 12428 intra-atom interactions NBONDS: found 12426 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=30185.978 E(kin)=6404.733 temperature=3173.814 | | Etotal =23781.244 grad(E)=94.183 E(BOND)=2554.945 E(ANGL)=5328.607 | | E(DIHE)=0.000 E(IMPR)=7209.835 E(VDW )=447.749 E(CDIH)=1247.507 | | E(NOE )=6728.038 E(PLAN)=264.563 | ------------------------------------------------------------------------------- NBONDS: found 12439 intra-atom interactions NBONDS: found 12415 intra-atom interactions NBONDS: found 12427 intra-atom interactions NBONDS: found 12440 intra-atom interactions NBONDS: found 12484 intra-atom interactions NBONDS: found 12485 intra-atom interactions NBONDS: found 12501 intra-atom interactions NBONDS: found 12498 intra-atom interactions NBONDS: found 12516 intra-atom interactions NBONDS: found 12518 intra-atom interactions NBONDS: found 12533 intra-atom interactions NBONDS: found 12531 intra-atom interactions NBONDS: found 12510 intra-atom interactions NBONDS: found 12519 intra-atom interactions NBONDS: found 12505 intra-atom interactions NBONDS: found 12462 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=31105.548 E(kin)=6653.984 temperature=3297.329 | | Etotal =24451.564 grad(E)=93.610 E(BOND)=2742.523 E(ANGL)=5905.324 | | E(DIHE)=0.000 E(IMPR)=7279.430 E(VDW )=246.581 E(CDIH)=1189.682 | | E(NOE )=6792.729 E(PLAN)=295.296 | ------------------------------------------------------------------------------- NBONDS: found 12386 intra-atom interactions NBONDS: found 12397 intra-atom interactions NBONDS: found 12412 intra-atom interactions NBONDS: found 12472 intra-atom interactions NBONDS: found 12474 intra-atom interactions NBONDS: found 12476 intra-atom interactions NBONDS: found 12460 intra-atom interactions NBONDS: found 12490 intra-atom interactions NBONDS: found 12504 intra-atom interactions NBONDS: found 12547 intra-atom interactions NBONDS: found 12570 intra-atom interactions NBONDS: found 12579 intra-atom interactions NBONDS: found 12579 intra-atom interactions NBONDS: found 12604 intra-atom interactions NBONDS: found 12595 intra-atom interactions NBONDS: found 12613 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=30405.638 E(kin)=6375.302 temperature=3159.230 | | Etotal =24030.336 grad(E)=94.882 E(BOND)=2706.894 E(ANGL)=5259.201 | | E(DIHE)=0.000 E(IMPR)=7508.629 E(VDW )=415.136 E(CDIH)=1205.959 | | E(NOE )=6623.370 E(PLAN)=311.147 | ------------------------------------------------------------------------------- NBONDS: found 12626 intra-atom interactions NBONDS: found 12640 intra-atom interactions NBONDS: found 12624 intra-atom interactions NBONDS: found 12609 intra-atom interactions NBONDS: found 12641 intra-atom interactions NBONDS: found 12665 intra-atom interactions NBONDS: found 12707 intra-atom interactions NBONDS: found 12749 intra-atom interactions NBONDS: found 12797 intra-atom interactions NBONDS: found 12830 intra-atom interactions NBONDS: found 12827 intra-atom interactions NBONDS: found 12846 intra-atom interactions NBONDS: found 12846 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=29423.324 E(kin)=6111.510 temperature=3028.510 | | Etotal =23311.814 grad(E)=95.170 E(BOND)=2560.514 E(ANGL)=5402.179 | | E(DIHE)=0.000 E(IMPR)=6808.093 E(VDW )=494.884 E(CDIH)=1302.181 | | E(NOE )=6533.379 E(PLAN)=210.584 | ------------------------------------------------------------------------------- NBONDS: found 12849 intra-atom interactions NBONDS: found 12832 intra-atom interactions NBONDS: found 12780 intra-atom interactions NBONDS: found 12782 intra-atom interactions NBONDS: found 12766 intra-atom interactions NBONDS: found 12781 intra-atom interactions NBONDS: found 12790 intra-atom interactions NBONDS: found 12814 intra-atom interactions NBONDS: found 12797 intra-atom interactions NBONDS: found 12797 intra-atom interactions NBONDS: found 12784 intra-atom interactions NBONDS: found 12746 intra-atom interactions NBONDS: found 12700 intra-atom interactions NBONDS: found 12705 intra-atom interactions NBONDS: found 12736 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=29481.577 E(kin)=6336.095 temperature=3139.801 | | Etotal =23145.482 grad(E)=92.539 E(BOND)=2874.032 E(ANGL)=4980.319 | | E(DIHE)=0.000 E(IMPR)=6995.512 E(VDW )=282.843 E(CDIH)=1385.625 | | E(NOE )=6374.083 E(PLAN)=253.068 | ------------------------------------------------------------------------------- NBONDS: found 12781 intra-atom interactions NBONDS: found 12813 intra-atom interactions NBONDS: found 12805 intra-atom interactions NBONDS: found 12762 intra-atom interactions NBONDS: found 12768 intra-atom interactions NBONDS: found 12779 intra-atom interactions NBONDS: found 12774 intra-atom interactions NBONDS: found 12726 intra-atom interactions NBONDS: found 12657 intra-atom interactions NBONDS: found 12640 intra-atom interactions NBONDS: found 12625 intra-atom interactions NBONDS: found 12665 intra-atom interactions NBONDS: found 12663 intra-atom interactions NBONDS: found 12645 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=29467.570 E(kin)=5621.516 temperature=2785.697 | | Etotal =23846.054 grad(E)=96.349 E(BOND)=2822.098 E(ANGL)=5354.305 | | E(DIHE)=0.000 E(IMPR)=7146.384 E(VDW )=443.976 E(CDIH)=1137.746 | | E(NOE )=6715.112 E(PLAN)=226.434 | ------------------------------------------------------------------------------- NBONDS: found 12631 intra-atom interactions NBONDS: found 12679 intra-atom interactions NBONDS: found 12675 intra-atom interactions NBONDS: found 12680 intra-atom interactions NBONDS: found 12662 intra-atom interactions NBONDS: found 12649 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00001 0.00001 0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> constraints inter (all) (all) weights * 0.2 dihe 0.2 impr 0.2 vdw 0.01 end end SELRPN: 677 atoms have been selected out of 677 SELRPN: 677 atoms have been selected out of 677 X-PLOR> parameter nbonds repel=0.9 end end X-PLOR> dynamics verlet DYNAmics> nstep=$nstep1 time=$high_timestep iasvel=current firstt=$init_t DYNAmics> tcoup=true tbath=$init_t nprint=100 iprfrq=0 DYNAmics> end DYNAMC: number of degrees of freedom= 2031 ASSVEL: current velocities taken. CENMAS: Information about center of free masses position [A] : 0.00001 0.00001 0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00001 0.00001 0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 CODBON: bond type-based parameters retrieved CODANG: angle type-based parameters retrieved CODIMP: improper type-based parameters retrieved NBUPDA: type-based van der Waals parameters retrieved. NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 728 exclusions and 0 interactions(1-4) NBONDS: found 12657 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=36301.313 E(kin)=6047.213 temperature=2996.648 | | Etotal =30254.100 grad(E)=108.321 E(BOND)=2801.205 E(ANGL)=5162.436 | | E(DIHE)=0.000 E(IMPR)=13932.291 E(VDW )=365.959 E(CDIH)=1291.891 | | E(NOE )=6435.365 E(PLAN)=264.953 | ------------------------------------------------------------------------------- NBONDS: found 12658 intra-atom interactions NBONDS: found 12718 intra-atom interactions NBONDS: found 12746 intra-atom interactions NBONDS: found 12769 intra-atom interactions NBONDS: found 12853 intra-atom interactions NBONDS: found 12899 intra-atom interactions NBONDS: found 12924 intra-atom interactions NBONDS: found 12937 intra-atom interactions NBONDS: found 13055 intra-atom interactions NBONDS: found 13100 intra-atom interactions NBONDS: found 13139 intra-atom interactions NBONDS: found 13159 intra-atom interactions NBONDS: found 13211 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=32172.932 E(kin)=6696.751 temperature=3318.521 | | Etotal =25476.181 grad(E)=96.176 E(BOND)=2869.479 E(ANGL)=7360.378 | | E(DIHE)=0.000 E(IMPR)=5193.124 E(VDW )=437.796 E(CDIH)=1527.582 | | E(NOE )=7833.849 E(PLAN)=253.974 | ------------------------------------------------------------------------------- NBONDS: found 13216 intra-atom interactions NBONDS: found 13245 intra-atom interactions NBONDS: found 13290 intra-atom interactions NBONDS: found 13375 intra-atom interactions NBONDS: found 13438 intra-atom interactions NBONDS: found 13546 intra-atom interactions NBONDS: found 13607 intra-atom interactions NBONDS: found 13640 intra-atom interactions NBONDS: found 13709 intra-atom interactions NBONDS: found 13740 intra-atom interactions NBONDS: found 13833 intra-atom interactions NBONDS: found 13871 intra-atom interactions NBONDS: found 13922 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=28727.395 E(kin)=6293.635 temperature=3118.760 | | Etotal =22433.760 grad(E)=91.179 E(BOND)=3071.778 E(ANGL)=5715.724 | | E(DIHE)=0.000 E(IMPR)=4290.042 E(VDW )=484.186 E(CDIH)=1340.948 | | E(NOE )=7256.887 E(PLAN)=274.195 | ------------------------------------------------------------------------------- NBONDS: found 13934 intra-atom interactions NBONDS: found 13987 intra-atom interactions NBONDS: found 14041 intra-atom interactions NBONDS: found 14144 intra-atom interactions NBONDS: found 14254 intra-atom interactions NBONDS: found 14348 intra-atom interactions NBONDS: found 14405 intra-atom interactions NBONDS: found 14476 intra-atom interactions NBONDS: found 14558 intra-atom interactions NBONDS: found 14673 intra-atom interactions NBONDS: found 14784 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=27432.879 E(kin)=5987.201 temperature=2966.910 | | Etotal =21445.677 grad(E)=87.685 E(BOND)=2953.261 E(ANGL)=5833.186 | | E(DIHE)=0.000 E(IMPR)=3586.202 E(VDW )=525.267 E(CDIH)=1374.034 | | E(NOE )=6977.719 E(PLAN)=196.008 | ------------------------------------------------------------------------------- NBONDS: found 14851 intra-atom interactions NBONDS: found 14912 intra-atom interactions NBONDS: found 15039 intra-atom interactions NBONDS: found 15123 intra-atom interactions NBONDS: found 15200 intra-atom interactions NBONDS: found 15231 intra-atom interactions NBONDS: found 15262 intra-atom interactions NBONDS: found 15327 intra-atom interactions NBONDS: found 15371 intra-atom interactions NBONDS: found 15407 intra-atom interactions NBONDS: found 15434 intra-atom interactions NBONDS: found 15429 intra-atom interactions NBONDS: found 15459 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=27825.002 E(kin)=6485.776 temperature=3213.974 | | Etotal =21339.226 grad(E)=90.964 E(BOND)=3171.148 E(ANGL)=5520.659 | | E(DIHE)=0.000 E(IMPR)=3539.176 E(VDW )=563.414 E(CDIH)=1154.755 | | E(NOE )=7163.562 E(PLAN)=226.512 | ------------------------------------------------------------------------------- NBONDS: found 15469 intra-atom interactions NBONDS: found 15592 intra-atom interactions NBONDS: found 15627 intra-atom interactions NBONDS: found 15642 intra-atom interactions NBONDS: found 15645 intra-atom interactions NBONDS: found 15647 intra-atom interactions NBONDS: found 15691 intra-atom interactions NBONDS: found 15721 intra-atom interactions NBONDS: found 15731 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=27267.738 E(kin)=6062.996 temperature=3004.469 | | Etotal =21204.742 grad(E)=92.308 E(BOND)=2699.386 E(ANGL)=5588.177 | | E(DIHE)=0.000 E(IMPR)=3921.464 E(VDW )=573.892 E(CDIH)=1236.425 | | E(NOE )=7014.952 E(PLAN)=170.444 | ------------------------------------------------------------------------------- NBONDS: found 15747 intra-atom interactions NBONDS: found 15777 intra-atom interactions NBONDS: found 15844 intra-atom interactions NBONDS: found 15915 intra-atom interactions NBONDS: found 15939 intra-atom interactions NBONDS: found 15986 intra-atom interactions NBONDS: found 16007 intra-atom interactions NBONDS: found 16072 intra-atom interactions NBONDS: found 16142 intra-atom interactions NBONDS: found 16197 intra-atom interactions NBONDS: found 16239 intra-atom interactions NBONDS: found 16298 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=26201.261 E(kin)=6245.813 temperature=3095.063 | | Etotal =19955.448 grad(E)=92.419 E(BOND)=2654.512 E(ANGL)=5075.025 | | E(DIHE)=0.000 E(IMPR)=2950.073 E(VDW )=594.675 E(CDIH)=1246.024 | | E(NOE )=7210.859 E(PLAN)=224.281 | ------------------------------------------------------------------------------- NBONDS: found 16317 intra-atom interactions NBONDS: found 16330 intra-atom interactions NBONDS: found 16366 intra-atom interactions NBONDS: found 16430 intra-atom interactions NBONDS: found 16430 intra-atom interactions NBONDS: found 16502 intra-atom interactions NBONDS: found 16535 intra-atom interactions NBONDS: found 16559 intra-atom interactions NBONDS: found 16635 intra-atom interactions NBONDS: found 16692 intra-atom interactions NBONDS: found 16729 intra-atom interactions NBONDS: found 16783 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=25889.826 E(kin)=5924.837 temperature=2936.005 | | Etotal =19964.989 grad(E)=95.633 E(BOND)=2844.378 E(ANGL)=5624.286 | | E(DIHE)=0.000 E(IMPR)=2848.340 E(VDW )=619.450 E(CDIH)=1038.593 | | E(NOE )=6854.184 E(PLAN)=135.758 | ------------------------------------------------------------------------------- NBONDS: found 16781 intra-atom interactions NBONDS: found 16820 intra-atom interactions NBONDS: found 16864 intra-atom interactions NBONDS: found 16980 intra-atom interactions NBONDS: found 16992 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00001 0.00001 0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> constraints inter (all) (all) weights * 0.4 dihe 0.4 impr 0.4 vdw 0.003 end end SELRPN: 677 atoms have been selected out of 677 SELRPN: 677 atoms have been selected out of 677 X-PLOR> parameter nbonds nbxmod=-3 end end X-PLOR> dynamics verlet DYNAmics> nstep=$nstep2 time=$high_timestep iasvel=current firstt=$init_t DYNAmics> tcoup=true tbath=$init_t nprint=100 iprfrq=0 DYNAmics> end DYNAMC: number of degrees of freedom= 2031 ASSVEL: current velocities taken. CENMAS: Information about center of free masses position [A] : 0.00001 0.00001 0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00001 0.00001 0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 CODBON: bond type-based parameters retrieved CODANG: angle type-based parameters retrieved CODIMP: improper type-based parameters retrieved NBUPDA: type-based van der Waals parameters retrieved. NBONDS: generating intra-molecular exclusion list with mode=-3 MAKINB: mode -3 found 2027 exclusions and 0 interactions(1-4) NBONDS: found 15744 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=36018.324 E(kin)=5917.043 temperature=2932.143 | | Etotal =30101.281 grad(E)=178.429 E(BOND)=5367.653 E(ANGL)=10666.402 | | E(DIHE)=0.000 E(IMPR)=5445.939 E(VDW )=133.127 E(CDIH)=1015.084 | | E(NOE )=7288.566 E(PLAN)=184.510 | ------------------------------------------------------------------------------- NBONDS: found 15737 intra-atom interactions NBONDS: found 15723 intra-atom interactions NBONDS: found 15716 intra-atom interactions NBONDS: found 15796 intra-atom interactions NBONDS: found 15804 intra-atom interactions NBONDS: found 15806 intra-atom interactions NBONDS: found 15862 intra-atom interactions NBONDS: found 15889 intra-atom interactions NBONDS: found 15931 intra-atom interactions NBONDS: found 15949 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=31014.223 E(kin)=6738.514 temperature=3339.217 | | Etotal =24275.709 grad(E)=130.619 E(BOND)=2687.663 E(ANGL)=6986.068 | | E(DIHE)=0.000 E(IMPR)=3224.843 E(VDW )=136.030 E(CDIH)=1215.873 | | E(NOE )=9804.451 E(PLAN)=220.780 | ------------------------------------------------------------------------------- NBONDS: found 16022 intra-atom interactions NBONDS: found 16032 intra-atom interactions NBONDS: found 16171 intra-atom interactions NBONDS: found 16230 intra-atom interactions NBONDS: found 16318 intra-atom interactions NBONDS: found 16381 intra-atom interactions NBONDS: found 16402 intra-atom interactions NBONDS: found 16471 intra-atom interactions NBONDS: found 16586 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=29672.800 E(kin)=6272.013 temperature=3108.046 | | Etotal =23400.787 grad(E)=124.155 E(BOND)=2944.911 E(ANGL)=6265.509 | | E(DIHE)=0.000 E(IMPR)=2699.757 E(VDW )=149.947 E(CDIH)=1243.830 | | E(NOE )=9864.898 E(PLAN)=231.936 | ------------------------------------------------------------------------------- NBONDS: found 16648 intra-atom interactions NBONDS: found 16716 intra-atom interactions NBONDS: found 16854 intra-atom interactions NBONDS: found 17030 intra-atom interactions NBONDS: found 17105 intra-atom interactions NBONDS: found 17178 intra-atom interactions NBONDS: found 17238 intra-atom interactions NBONDS: found 17290 intra-atom interactions NBONDS: found 17396 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=28922.355 E(kin)=6077.757 temperature=3011.784 | | Etotal =22844.598 grad(E)=121.628 E(BOND)=2573.439 E(ANGL)=6113.167 | | E(DIHE)=0.000 E(IMPR)=2967.828 E(VDW )=170.968 E(CDIH)=1332.946 | | E(NOE )=9451.473 E(PLAN)=234.776 | ------------------------------------------------------------------------------- NBONDS: found 17486 intra-atom interactions NBONDS: found 17557 intra-atom interactions NBONDS: found 17687 intra-atom interactions NBONDS: found 17750 intra-atom interactions NBONDS: found 17883 intra-atom interactions NBONDS: found 18113 intra-atom interactions NBONDS: found 18273 intra-atom interactions NBONDS: found 18418 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=28674.659 E(kin)=6158.028 temperature=3051.561 | | Etotal =22516.631 grad(E)=127.621 E(BOND)=2726.739 E(ANGL)=6170.955 | | E(DIHE)=0.000 E(IMPR)=2838.855 E(VDW )=192.413 E(CDIH)=1341.401 | | E(NOE )=9018.085 E(PLAN)=228.183 | ------------------------------------------------------------------------------- NBONDS: found 18532 intra-atom interactions NBONDS: found 18579 intra-atom interactions NBONDS: found 18594 intra-atom interactions NBONDS: found 18537 intra-atom interactions NBONDS: found 18511 intra-atom interactions NBONDS: found 18544 intra-atom interactions NBONDS: found 18546 intra-atom interactions NBONDS: found 18520 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=28254.123 E(kin)=6423.317 temperature=3183.023 | | Etotal =21830.806 grad(E)=119.104 E(BOND)=2543.270 E(ANGL)=6046.791 | | E(DIHE)=0.000 E(IMPR)=2991.735 E(VDW )=202.166 E(CDIH)=1192.649 | | E(NOE )=8650.284 E(PLAN)=203.911 | ------------------------------------------------------------------------------- NBONDS: found 18464 intra-atom interactions NBONDS: found 18406 intra-atom interactions NBONDS: found 18459 intra-atom interactions NBONDS: found 18569 intra-atom interactions NBONDS: found 18652 intra-atom interactions NBONDS: found 18735 intra-atom interactions NBONDS: found 18869 intra-atom interactions NBONDS: found 18971 intra-atom interactions NBONDS: found 19086 intra-atom interactions NBONDS: found 19114 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=27801.507 E(kin)=6055.010 temperature=3000.512 | | Etotal =21746.497 grad(E)=127.530 E(BOND)=2314.060 E(ANGL)=5483.084 | | E(DIHE)=0.000 E(IMPR)=3332.760 E(VDW )=211.716 E(CDIH)=1106.695 | | E(NOE )=9065.851 E(PLAN)=232.332 | ------------------------------------------------------------------------------- NBONDS: found 19167 intra-atom interactions NBONDS: found 19321 intra-atom interactions NBONDS: found 19348 intra-atom interactions NBONDS: found 19341 intra-atom interactions NBONDS: found 19414 intra-atom interactions NBONDS: found 19483 intra-atom interactions NBONDS: found 19556 intra-atom interactions NBONDS: found 19626 intra-atom interactions NBONDS: found 19701 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=27488.845 E(kin)=6199.018 temperature=3071.874 | | Etotal =21289.827 grad(E)=122.983 E(BOND)=2413.578 E(ANGL)=5153.443 | | E(DIHE)=0.000 E(IMPR)=3072.760 E(VDW )=220.004 E(CDIH)=1178.484 | | E(NOE )=8984.612 E(PLAN)=266.944 | ------------------------------------------------------------------------------- NBONDS: found 19795 intra-atom interactions NBONDS: found 19835 intra-atom interactions NBONDS: found 19976 intra-atom interactions NBONDS: found 20109 intra-atom interactions NBONDS: found 20125 intra-atom interactions NBONDS: found 20106 intra-atom interactions NBONDS: found 19955 intra-atom interactions NBONDS: found 19910 intra-atom interactions NBONDS: found 19908 intra-atom interactions --------------- step= 800 at 1.60000 ps -------------------------------- | E(kin)+E(total)=27003.196 E(kin)=6870.564 temperature=3404.653 | | Etotal =20132.633 grad(E)=112.632 E(BOND)=2641.527 E(ANGL)=5170.596 | | E(DIHE)=0.000 E(IMPR)=2979.254 E(VDW )=227.828 E(CDIH)=1164.712 | | E(NOE )=7680.739 E(PLAN)=267.977 | ------------------------------------------------------------------------------- NBONDS: found 19894 intra-atom interactions NBONDS: found 19864 intra-atom interactions NBONDS: found 19823 intra-atom interactions NBONDS: found 19777 intra-atom interactions NBONDS: found 19821 intra-atom interactions NBONDS: found 19788 intra-atom interactions NBONDS: found 19774 intra-atom interactions NBONDS: found 19892 intra-atom interactions NBONDS: found 19937 intra-atom interactions NBONDS: found 19943 intra-atom interactions NBONDS: found 19952 intra-atom interactions --------------- step= 900 at 1.80000 ps -------------------------------- | E(kin)+E(total)=26060.284 E(kin)=6099.590 temperature=3022.603 | | Etotal =19960.694 grad(E)=112.159 E(BOND)=2608.857 E(ANGL)=5588.260 | | E(DIHE)=0.000 E(IMPR)=2638.866 E(VDW )=230.418 E(CDIH)=1120.028 | | E(NOE )=7498.141 E(PLAN)=276.123 | ------------------------------------------------------------------------------- NBONDS: found 19942 intra-atom interactions NBONDS: found 20014 intra-atom interactions NBONDS: found 20059 intra-atom interactions NBONDS: found 20093 intra-atom interactions NBONDS: found 20148 intra-atom interactions NBONDS: found 20133 intra-atom interactions NBONDS: found 20111 intra-atom interactions NBONDS: found 20040 intra-atom interactions NBONDS: found 20059 intra-atom interactions --------------- step= 1000 at 2.00000 ps -------------------------------- | E(kin)+E(total)=25689.202 E(kin)=5922.476 temperature=2934.836 | | Etotal =19766.726 grad(E)=113.969 E(BOND)=2593.737 E(ANGL)=5438.547 | | E(DIHE)=0.000 E(IMPR)=2432.557 E(VDW )=229.010 E(CDIH)=997.242 | | E(NOE )=7830.059 E(PLAN)=245.574 | ------------------------------------------------------------------------------- NBONDS: found 20095 intra-atom interactions NBONDS: found 20097 intra-atom interactions NBONDS: found 20027 intra-atom interactions NBONDS: found 20025 intra-atom interactions NBONDS: found 19969 intra-atom interactions NBONDS: found 19935 intra-atom interactions NBONDS: found 19939 intra-atom interactions NBONDS: found 19937 intra-atom interactions NBONDS: found 19851 intra-atom interactions NBONDS: found 19873 intra-atom interactions NBONDS: found 19812 intra-atom interactions --------------- step= 1100 at 2.20000 ps -------------------------------- | E(kin)+E(total)=25816.414 E(kin)=6057.628 temperature=3001.809 | | Etotal =19758.786 grad(E)=114.931 E(BOND)=2531.658 E(ANGL)=5456.888 | | E(DIHE)=0.000 E(IMPR)=2705.795 E(VDW )=224.261 E(CDIH)=1130.748 | | E(NOE )=7457.444 E(PLAN)=251.992 | ------------------------------------------------------------------------------- NBONDS: found 19767 intra-atom interactions NBONDS: found 19798 intra-atom interactions NBONDS: found 19785 intra-atom interactions NBONDS: found 19812 intra-atom interactions NBONDS: found 19826 intra-atom interactions NBONDS: found 19830 intra-atom interactions NBONDS: found 19835 intra-atom interactions NBONDS: found 19856 intra-atom interactions NBONDS: found 19843 intra-atom interactions NBONDS: found 19870 intra-atom interactions NBONDS: found 19903 intra-atom interactions NBONDS: found 19859 intra-atom interactions NBONDS: found 19819 intra-atom interactions NBONDS: found 19775 intra-atom interactions NBONDS: found 19767 intra-atom interactions NBONDS: found 19777 intra-atom interactions NBONDS: found 19747 intra-atom interactions NBONDS: found 19762 intra-atom interactions --------------- step= 1200 at 2.40000 ps -------------------------------- | E(kin)+E(total)=25922.705 E(kin)=6484.384 temperature=3213.285 | | Etotal =19438.321 grad(E)=125.771 E(BOND)=2433.113 E(ANGL)=5385.740 | | E(DIHE)=0.000 E(IMPR)=1969.257 E(VDW )=230.309 E(CDIH)=1047.145 | | E(NOE )=8147.007 E(PLAN)=225.749 | ------------------------------------------------------------------------------- NBONDS: found 19771 intra-atom interactions NBONDS: found 19718 intra-atom interactions NBONDS: found 19643 intra-atom interactions NBONDS: found 19569 intra-atom interactions NBONDS: found 19418 intra-atom interactions NBONDS: found 19317 intra-atom interactions NBONDS: found 19312 intra-atom interactions NBONDS: found 19211 intra-atom interactions NBONDS: found 19159 intra-atom interactions NBONDS: found 19047 intra-atom interactions NBONDS: found 18970 intra-atom interactions --------------- step= 1300 at 2.60000 ps -------------------------------- | E(kin)+E(total)=25260.918 E(kin)=5817.558 temperature=2882.844 | | Etotal =19443.360 grad(E)=132.503 E(BOND)=2427.084 E(ANGL)=5081.121 | | E(DIHE)=0.000 E(IMPR)=1684.238 E(VDW )=209.058 E(CDIH)=965.958 | | E(NOE )=8835.484 E(PLAN)=240.418 | ------------------------------------------------------------------------------- NBONDS: found 18942 intra-atom interactions NBONDS: found 18838 intra-atom interactions NBONDS: found 18744 intra-atom interactions NBONDS: found 18619 intra-atom interactions NBONDS: found 18543 intra-atom interactions NBONDS: found 18449 intra-atom interactions NBONDS: found 18361 intra-atom interactions NBONDS: found 18198 intra-atom interactions NBONDS: found 18085 intra-atom interactions NBONDS: found 17949 intra-atom interactions NBONDS: found 17882 intra-atom interactions --------------- step= 1400 at 2.80000 ps -------------------------------- | E(kin)+E(total)=24735.456 E(kin)=5764.414 temperature=2856.509 | | Etotal =18971.043 grad(E)=127.257 E(BOND)=2395.054 E(ANGL)=5488.387 | | E(DIHE)=0.000 E(IMPR)=1609.544 E(VDW )=182.333 E(CDIH)=891.521 | | E(NOE )=8149.269 E(PLAN)=254.933 | ------------------------------------------------------------------------------- NBONDS: found 17790 intra-atom interactions NBONDS: found 17713 intra-atom interactions NBONDS: found 17632 intra-atom interactions NBONDS: found 17613 intra-atom interactions NBONDS: found 17581 intra-atom interactions NBONDS: found 17530 intra-atom interactions NBONDS: found 17467 intra-atom interactions NBONDS: found 17401 intra-atom interactions NBONDS: found 17374 intra-atom interactions NBONDS: found 17316 intra-atom interactions --------------- step= 1500 at 3.00000 ps -------------------------------- | E(kin)+E(total)=24407.096 E(kin)=6026.678 temperature=2986.472 | | Etotal =18380.419 grad(E)=116.750 E(BOND)=2573.811 E(ANGL)=4632.365 | | E(DIHE)=0.000 E(IMPR)=1418.823 E(VDW )=173.353 E(CDIH)=1013.111 | | E(NOE )=8309.449 E(PLAN)=259.506 | ------------------------------------------------------------------------------- NBONDS: found 17193 intra-atom interactions NBONDS: found 17185 intra-atom interactions NBONDS: found 17187 intra-atom interactions NBONDS: found 17186 intra-atom interactions NBONDS: found 17110 intra-atom interactions NBONDS: found 17132 intra-atom interactions NBONDS: found 17063 intra-atom interactions NBONDS: found 17054 intra-atom interactions NBONDS: found 17060 intra-atom interactions NBONDS: found 17028 intra-atom interactions NBONDS: found 16999 intra-atom interactions --------------- step= 1600 at 3.20000 ps -------------------------------- | E(kin)+E(total)=23890.342 E(kin)=6189.413 temperature=3067.114 | | Etotal =17700.929 grad(E)=118.092 E(BOND)=2396.579 E(ANGL)=4557.426 | | E(DIHE)=0.000 E(IMPR)=1705.161 E(VDW )=164.813 E(CDIH)=948.416 | | E(NOE )=7683.558 E(PLAN)=244.977 | ------------------------------------------------------------------------------- NBONDS: found 17001 intra-atom interactions NBONDS: found 16941 intra-atom interactions NBONDS: found 16972 intra-atom interactions NBONDS: found 16943 intra-atom interactions NBONDS: found 16874 intra-atom interactions NBONDS: found 16874 intra-atom interactions NBONDS: found 16814 intra-atom interactions NBONDS: found 16772 intra-atom interactions NBONDS: found 16805 intra-atom interactions NBONDS: found 16756 intra-atom interactions --------------- step= 1700 at 3.40000 ps -------------------------------- | E(kin)+E(total)=23436.938 E(kin)=5778.281 temperature=2863.381 | | Etotal =17658.657 grad(E)=119.906 E(BOND)=2756.412 E(ANGL)=4585.667 | | E(DIHE)=0.000 E(IMPR)=1357.103 E(VDW )=168.000 E(CDIH)=735.664 | | E(NOE )=7670.886 E(PLAN)=384.926 | ------------------------------------------------------------------------------- NBONDS: found 16769 intra-atom interactions NBONDS: found 16802 intra-atom interactions NBONDS: found 16766 intra-atom interactions NBONDS: found 16729 intra-atom interactions NBONDS: found 16742 intra-atom interactions NBONDS: found 16666 intra-atom interactions NBONDS: found 16697 intra-atom interactions NBONDS: found 16726 intra-atom interactions NBONDS: found 16715 intra-atom interactions --------------- step= 1800 at 3.60000 ps -------------------------------- | E(kin)+E(total)=23285.599 E(kin)=6105.785 temperature=3025.673 | | Etotal =17179.815 grad(E)=110.970 E(BOND)=2679.630 E(ANGL)=4322.934 | | E(DIHE)=0.000 E(IMPR)=1487.182 E(VDW )=167.279 E(CDIH)=906.282 | | E(NOE )=7274.660 E(PLAN)=341.847 | ------------------------------------------------------------------------------- NBONDS: found 16744 intra-atom interactions NBONDS: found 16832 intra-atom interactions NBONDS: found 16814 intra-atom interactions NBONDS: found 16818 intra-atom interactions NBONDS: found 16782 intra-atom interactions NBONDS: found 16709 intra-atom interactions NBONDS: found 16634 intra-atom interactions NBONDS: found 16612 intra-atom interactions NBONDS: found 16620 intra-atom interactions NBONDS: found 16604 intra-atom interactions --------------- step= 1900 at 3.80000 ps -------------------------------- | E(kin)+E(total)=23145.641 E(kin)=6151.918 temperature=3048.534 | | Etotal =16993.723 grad(E)=110.763 E(BOND)=2437.651 E(ANGL)=4637.769 | | E(DIHE)=0.000 E(IMPR)=1484.018 E(VDW )=165.220 E(CDIH)=909.735 | | E(NOE )=7002.762 E(PLAN)=356.568 | ------------------------------------------------------------------------------- NBONDS: found 16628 intra-atom interactions NBONDS: found 16711 intra-atom interactions NBONDS: found 16762 intra-atom interactions NBONDS: found 16740 intra-atom interactions NBONDS: found 16777 intra-atom interactions NBONDS: found 16843 intra-atom interactions NBONDS: found 16965 intra-atom interactions NBONDS: found 17059 intra-atom interactions NBONDS: found 17136 intra-atom interactions NBONDS: found 17243 intra-atom interactions --------------- step= 2000 at 4.00000 ps -------------------------------- | E(kin)+E(total)=22982.758 E(kin)=6122.255 temperature=3033.834 | | Etotal =16860.503 grad(E)=110.684 E(BOND)=2428.723 E(ANGL)=4548.862 | | E(DIHE)=0.000 E(IMPR)=1429.773 E(VDW )=172.446 E(CDIH)=723.726 | | E(NOE )=7190.107 E(PLAN)=366.867 | ------------------------------------------------------------------------------- NBONDS: found 17191 intra-atom interactions NBONDS: found 17233 intra-atom interactions NBONDS: found 17229 intra-atom interactions NBONDS: found 17293 intra-atom interactions NBONDS: found 17383 intra-atom interactions NBONDS: found 17412 intra-atom interactions NBONDS: found 17491 intra-atom interactions NBONDS: found 17508 intra-atom interactions NBONDS: found 17524 intra-atom interactions NBONDS: found 17531 intra-atom interactions --------------- step= 2100 at 4.20000 ps -------------------------------- | E(kin)+E(total)=22882.482 E(kin)=6261.864 temperature=3103.017 | | Etotal =16620.618 grad(E)=109.118 E(BOND)=2417.094 E(ANGL)=4616.982 | | E(DIHE)=0.000 E(IMPR)=1326.336 E(VDW )=173.897 E(CDIH)=842.965 | | E(NOE )=6884.470 E(PLAN)=358.874 | ------------------------------------------------------------------------------- NBONDS: found 17556 intra-atom interactions NBONDS: found 17626 intra-atom interactions NBONDS: found 17740 intra-atom interactions NBONDS: found 17844 intra-atom interactions NBONDS: found 17894 intra-atom interactions NBONDS: found 18015 intra-atom interactions NBONDS: found 18110 intra-atom interactions NBONDS: found 18155 intra-atom interactions NBONDS: found 18330 intra-atom interactions --------------- step= 2200 at 4.40000 ps -------------------------------- | E(kin)+E(total)=22864.808 E(kin)=6087.078 temperature=3016.403 | | Etotal =16777.730 grad(E)=116.058 E(BOND)=2434.640 E(ANGL)=4472.178 | | E(DIHE)=0.000 E(IMPR)=1482.120 E(VDW )=189.104 E(CDIH)=864.706 | | E(NOE )=7004.637 E(PLAN)=330.346 | ------------------------------------------------------------------------------- NBONDS: found 18390 intra-atom interactions NBONDS: found 18560 intra-atom interactions NBONDS: found 18696 intra-atom interactions NBONDS: found 18797 intra-atom interactions NBONDS: found 18961 intra-atom interactions NBONDS: found 19063 intra-atom interactions NBONDS: found 19148 intra-atom interactions NBONDS: found 19271 intra-atom interactions NBONDS: found 19348 intra-atom interactions NBONDS: found 19469 intra-atom interactions --------------- step= 2300 at 4.60000 ps -------------------------------- | E(kin)+E(total)=23034.313 E(kin)=5946.729 temperature=2946.854 | | Etotal =17087.585 grad(E)=116.289 E(BOND)=2283.249 E(ANGL)=4883.723 | | E(DIHE)=0.000 E(IMPR)=1314.123 E(VDW )=208.634 E(CDIH)=949.591 | | E(NOE )=7147.226 E(PLAN)=301.039 | ------------------------------------------------------------------------------- NBONDS: found 19570 intra-atom interactions NBONDS: found 19601 intra-atom interactions NBONDS: found 19700 intra-atom interactions NBONDS: found 19804 intra-atom interactions NBONDS: found 19908 intra-atom interactions NBONDS: found 20055 intra-atom interactions NBONDS: found 20212 intra-atom interactions NBONDS: found 20337 intra-atom interactions NBONDS: found 20433 intra-atom interactions NBONDS: found 20519 intra-atom interactions --------------- step= 2400 at 4.80000 ps -------------------------------- | E(kin)+E(total)=23149.403 E(kin)=6000.368 temperature=2973.434 | | Etotal =17149.035 grad(E)=115.345 E(BOND)=2158.062 E(ANGL)=4743.878 | | E(DIHE)=0.000 E(IMPR)=1210.767 E(VDW )=230.554 E(CDIH)=866.363 | | E(NOE )=7627.521 E(PLAN)=311.889 | ------------------------------------------------------------------------------- NBONDS: found 20614 intra-atom interactions NBONDS: found 20756 intra-atom interactions NBONDS: found 20796 intra-atom interactions NBONDS: found 20859 intra-atom interactions NBONDS: found 20807 intra-atom interactions NBONDS: found 20837 intra-atom interactions NBONDS: found 20913 intra-atom interactions NBONDS: found 20927 intra-atom interactions NBONDS: found 20941 intra-atom interactions NBONDS: found 20939 intra-atom interactions NBONDS: found 20931 intra-atom interactions --------------- step= 2500 at 5.00000 ps -------------------------------- | E(kin)+E(total)=22880.918 E(kin)=6145.310 temperature=3045.259 | | Etotal =16735.609 grad(E)=138.780 E(BOND)=2621.440 E(ANGL)=4672.690 | | E(DIHE)=0.000 E(IMPR)=1339.165 E(VDW )=234.449 E(CDIH)=810.218 | | E(NOE )=6739.857 E(PLAN)=317.790 | ------------------------------------------------------------------------------- NBONDS: found 20961 intra-atom interactions NBONDS: found 21017 intra-atom interactions NBONDS: found 21086 intra-atom interactions NBONDS: found 21243 intra-atom interactions NBONDS: found 21320 intra-atom interactions NBONDS: found 21330 intra-atom interactions NBONDS: found 21349 intra-atom interactions NBONDS: found 21460 intra-atom interactions NBONDS: found 21329 intra-atom interactions NBONDS: found 21319 intra-atom interactions --------------- step= 2600 at 5.20000 ps -------------------------------- | E(kin)+E(total)=22963.191 E(kin)=5908.578 temperature=2927.949 | | Etotal =17054.613 grad(E)=119.831 E(BOND)=2480.219 E(ANGL)=5169.628 | | E(DIHE)=0.000 E(IMPR)=1251.815 E(VDW )=240.398 E(CDIH)=822.319 | | E(NOE )=6820.824 E(PLAN)=269.409 | ------------------------------------------------------------------------------- NBONDS: found 21395 intra-atom interactions NBONDS: found 21455 intra-atom interactions NBONDS: found 21495 intra-atom interactions NBONDS: found 21551 intra-atom interactions NBONDS: found 21576 intra-atom interactions NBONDS: found 21597 intra-atom interactions NBONDS: found 21734 intra-atom interactions NBONDS: found 21783 intra-atom interactions --------------- step= 2700 at 5.40000 ps -------------------------------- | E(kin)+E(total)=22908.994 E(kin)=6177.089 temperature=3061.007 | | Etotal =16731.905 grad(E)=119.004 E(BOND)=2436.293 E(ANGL)=4563.059 | | E(DIHE)=0.000 E(IMPR)=1368.570 E(VDW )=251.864 E(CDIH)=910.684 | | E(NOE )=6900.406 E(PLAN)=301.029 | ------------------------------------------------------------------------------- NBONDS: found 21840 intra-atom interactions NBONDS: found 21940 intra-atom interactions NBONDS: found 22080 intra-atom interactions NBONDS: found 22226 intra-atom interactions NBONDS: found 22337 intra-atom interactions NBONDS: found 22428 intra-atom interactions NBONDS: found 22580 intra-atom interactions NBONDS: found 22626 intra-atom interactions --------------- step= 2800 at 5.60000 ps -------------------------------- | E(kin)+E(total)=22778.491 E(kin)=5994.150 temperature=2970.353 | | Etotal =16784.341 grad(E)=117.712 E(BOND)=2166.985 E(ANGL)=4855.126 | | E(DIHE)=0.000 E(IMPR)=1283.275 E(VDW )=264.043 E(CDIH)=828.718 | | E(NOE )=7071.240 E(PLAN)=314.954 | ------------------------------------------------------------------------------- NBONDS: found 22562 intra-atom interactions NBONDS: found 22542 intra-atom interactions NBONDS: found 22505 intra-atom interactions NBONDS: found 22496 intra-atom interactions NBONDS: found 22505 intra-atom interactions NBONDS: found 22519 intra-atom interactions NBONDS: found 22563 intra-atom interactions NBONDS: found 22620 intra-atom interactions NBONDS: found 22628 intra-atom interactions --------------- step= 2900 at 5.80000 ps -------------------------------- | E(kin)+E(total)=22808.132 E(kin)=6051.399 temperature=2998.722 | | Etotal =16756.734 grad(E)=117.305 E(BOND)=2355.232 E(ANGL)=4908.582 | | E(DIHE)=0.000 E(IMPR)=1168.187 E(VDW )=267.833 E(CDIH)=897.019 | | E(NOE )=6884.078 E(PLAN)=275.803 | ------------------------------------------------------------------------------- NBONDS: found 22636 intra-atom interactions NBONDS: found 22630 intra-atom interactions NBONDS: found 22692 intra-atom interactions NBONDS: found 22758 intra-atom interactions NBONDS: found 22768 intra-atom interactions NBONDS: found 22769 intra-atom interactions NBONDS: found 22780 intra-atom interactions NBONDS: found 22661 intra-atom interactions --------------- step= 3000 at 6.00000 ps -------------------------------- | E(kin)+E(total)=23000.480 E(kin)=6151.301 temperature=3048.228 | | Etotal =16849.179 grad(E)=119.173 E(BOND)=2498.753 E(ANGL)=4938.301 | | E(DIHE)=0.000 E(IMPR)=1220.273 E(VDW )=269.076 E(CDIH)=892.946 | | E(NOE )=6725.515 E(PLAN)=304.316 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 0.00001 0.00001 0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> constraints inter (all) (all) weights * 1 dihe 1 impr 1 vdw 0.003 end end SELRPN: 677 atoms have been selected out of 677 SELRPN: 677 atoms have been selected out of 677 X-PLOR> dynamics verlet DYNAmics> nstep=$nstep1 time=$high_timestep iasvel=current firstt=$init_t DYNAmics> tcoup=true tbath=$init_t nprint=100 iprfrq=0 DYNAmics> end DYNAMC: number of degrees of freedom= 2031 ASSVEL: current velocities taken. CENMAS: Information about center of free masses position [A] : 0.00001 0.00001 0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00001 0.00001 0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 NBONDS: generating intra-molecular exclusion list with mode=-3 MAKINB: mode -3 found 2027 exclusions and 0 interactions(1-4) NBONDS: found 22473 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=35986.470 E(kin)=6151.301 temperature=3048.228 | | Etotal =29835.169 grad(E)=294.060 E(BOND)=6246.882 E(ANGL)=12345.753 | | E(DIHE)=0.000 E(IMPR)=3050.681 E(VDW )=269.076 E(CDIH)=892.946 | | E(NOE )=6725.515 E(PLAN)=304.316 | ------------------------------------------------------------------------------- NBONDS: found 22575 intra-atom interactions NBONDS: found 22588 intra-atom interactions NBONDS: found 22602 intra-atom interactions NBONDS: found 22606 intra-atom interactions NBONDS: found 22504 intra-atom interactions NBONDS: found 22427 intra-atom interactions NBONDS: found 22432 intra-atom interactions NBONDS: found 22436 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=28708.338 E(kin)=6599.242 temperature=3270.202 | | Etotal =22109.095 grad(E)=201.690 E(BOND)=2592.912 E(ANGL)=6988.467 | | E(DIHE)=0.000 E(IMPR)=1727.294 E(VDW )=272.390 E(CDIH)=919.126 | | E(NOE )=9234.249 E(PLAN)=374.658 | ------------------------------------------------------------------------------- NBONDS: found 22508 intra-atom interactions NBONDS: found 22604 intra-atom interactions NBONDS: found 22609 intra-atom interactions NBONDS: found 22635 intra-atom interactions NBONDS: found 22742 intra-atom interactions NBONDS: found 22747 intra-atom interactions NBONDS: found 22659 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=28007.163 E(kin)=6153.684 temperature=3049.409 | | Etotal =21853.478 grad(E)=192.505 E(BOND)=2644.817 E(ANGL)=6606.118 | | E(DIHE)=0.000 E(IMPR)=1494.951 E(VDW )=275.856 E(CDIH)=940.488 | | E(NOE )=9525.008 E(PLAN)=366.241 | ------------------------------------------------------------------------------- NBONDS: found 22555 intra-atom interactions NBONDS: found 22485 intra-atom interactions NBONDS: found 22340 intra-atom interactions NBONDS: found 22286 intra-atom interactions NBONDS: found 22338 intra-atom interactions NBONDS: found 22340 intra-atom interactions NBONDS: found 22385 intra-atom interactions NBONDS: found 22352 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=27577.043 E(kin)=6065.901 temperature=3005.909 | | Etotal =21511.143 grad(E)=193.962 E(BOND)=2555.154 E(ANGL)=7041.030 | | E(DIHE)=0.000 E(IMPR)=1543.842 E(VDW )=264.902 E(CDIH)=958.358 | | E(NOE )=8778.419 E(PLAN)=369.438 | ------------------------------------------------------------------------------- NBONDS: found 22522 intra-atom interactions NBONDS: found 22595 intra-atom interactions NBONDS: found 22581 intra-atom interactions NBONDS: found 22583 intra-atom interactions NBONDS: found 22587 intra-atom interactions NBONDS: found 22477 intra-atom interactions NBONDS: found 22402 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=27617.803 E(kin)=6092.703 temperature=3019.190 | | Etotal =21525.100 grad(E)=190.913 E(BOND)=2835.817 E(ANGL)=6575.274 | | E(DIHE)=0.000 E(IMPR)=1620.053 E(VDW )=264.593 E(CDIH)=1015.398 | | E(NOE )=8891.241 E(PLAN)=322.724 | ------------------------------------------------------------------------------- NBONDS: found 22336 intra-atom interactions NBONDS: found 22232 intra-atom interactions NBONDS: found 22161 intra-atom interactions NBONDS: found 22078 intra-atom interactions NBONDS: found 22004 intra-atom interactions NBONDS: found 21968 intra-atom interactions NBONDS: found 21838 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=27450.131 E(kin)=5863.118 temperature=2905.421 | | Etotal =21587.013 grad(E)=197.689 E(BOND)=2753.348 E(ANGL)=6624.302 | | E(DIHE)=0.000 E(IMPR)=1362.190 E(VDW )=265.205 E(CDIH)=904.700 | | E(NOE )=9278.949 E(PLAN)=398.319 | ------------------------------------------------------------------------------- NBONDS: found 21818 intra-atom interactions NBONDS: found 21721 intra-atom interactions NBONDS: found 21696 intra-atom interactions NBONDS: found 21605 intra-atom interactions NBONDS: found 21400 intra-atom interactions NBONDS: found 21324 intra-atom interactions NBONDS: found 21196 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=27727.111 E(kin)=5830.498 temperature=2889.256 | | Etotal =21896.613 grad(E)=199.781 E(BOND)=2588.248 E(ANGL)=6558.106 | | E(DIHE)=0.000 E(IMPR)=1657.442 E(VDW )=257.714 E(CDIH)=998.838 | | E(NOE )=9461.038 E(PLAN)=375.228 | ------------------------------------------------------------------------------- NBONDS: found 21026 intra-atom interactions NBONDS: found 20897 intra-atom interactions NBONDS: found 20719 intra-atom interactions NBONDS: found 20480 intra-atom interactions NBONDS: found 20449 intra-atom interactions NBONDS: found 20387 intra-atom interactions NBONDS: found 20396 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=27597.487 E(kin)=5949.064 temperature=2948.011 | | Etotal =21648.424 grad(E)=204.720 E(BOND)=2586.032 E(ANGL)=6775.998 | | E(DIHE)=0.000 E(IMPR)=1618.092 E(VDW )=245.238 E(CDIH)=900.243 | | E(NOE )=9144.612 E(PLAN)=378.208 | ------------------------------------------------------------------------------- NBONDS: found 20428 intra-atom interactions NBONDS: found 20319 intra-atom interactions NBONDS: found 20337 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00001 0.00001 0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> if ($image=1) then NEXTCD: condition evaluated as true X-PLOR> vector do (store7=x) (all) ! Store first image in stores. SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store8=y) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store9=z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store4=vx) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store5=vy) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store6=vz) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> end if X-PLOR> X-PLOR>end loop imag X-PLOR>for $image in (1 -1) loop imag FOR LOOP: symbol IMAGE set to -1.00000 (real) X-PLOR> X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates COOR>REMARK FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/dg.pdb" COOR>REMARK DATE:16-Aug-96 16:19:36 created by user: COOR>ATOM 1 P GUA 1 13.124 3.955 8.029 1.00 0.00 A COOR>ATOM 2 O1P GUA 1 12.913 3.265 8.771 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 = 2.8345 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.8514 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0467 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1070 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1273 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8713 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1403 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.3482 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0712 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.0843 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.3381 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.3226 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.9057 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.1430 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.3056 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8945 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.6008 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.6744 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.4466 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8712 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.7140 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 15411 intra-atom interactions NBONDS: found 15460 intra-atom interactions NBONDS: found 15542 intra-atom interactions NBONDS: found 15614 intra-atom interactions NBONDS: found 15709 intra-atom interactions NBONDS: found 15786 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0002 ----------------------- | Etotal =115178.577 grad(E)=360.458 E(BOND)=16973.248 E(VDW )=12715.673 | | E(CDIH)=4329.477 E(NOE )=80589.932 E(PLAN)=570.247 | ------------------------------------------------------------------------------- NBONDS: found 15802 intra-atom interactions NBONDS: found 15886 intra-atom interactions NBONDS: found 15883 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0002 ----------------------- | Etotal =62162.973 grad(E)=180.332 E(BOND)=5432.282 E(VDW )=9438.535 | | E(CDIH)=3189.041 E(NOE )=43719.833 E(PLAN)=383.282 | ------------------------------------------------------------------------------- NBONDS: found 15861 intra-atom interactions NBONDS: found 15849 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =43178.184 grad(E)=130.068 E(BOND)=2625.217 E(VDW )=7226.347 | | E(CDIH)=2835.486 E(NOE )=30226.400 E(PLAN)=264.735 | ------------------------------------------------------------------------------- NBONDS: found 15696 intra-atom interactions NBONDS: found 15678 intra-atom interactions NBONDS: found 15582 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0002 ----------------------- | Etotal =31854.498 grad(E)=112.641 E(BOND)=1737.944 E(VDW )=5150.420 | | E(CDIH)=2108.665 E(NOE )=22569.772 E(PLAN)=287.696 | ------------------------------------------------------------------------------- NBONDS: found 15452 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =27182.102 grad(E)=71.735 E(BOND)=956.467 E(VDW )=4331.361 | | E(CDIH)=1841.198 E(NOE )=19765.675 E(PLAN)=287.401 | ------------------------------------------------------------------------------- NBONDS: found 15363 intra-atom interactions --------------- cycle= 60 ------ stepsize= -0.0001 ----------------------- | Etotal =23692.095 grad(E)=74.909 E(BOND)=780.293 E(VDW )=3374.285 | | E(CDIH)=2244.104 E(NOE )=17049.794 E(PLAN)=243.617 | ------------------------------------------------------------------------------- NBONDS: found 15253 intra-atom interactions NBONDS: found 15143 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =21189.258 grad(E)=49.235 E(BOND)=826.996 E(VDW )=2990.212 | | E(CDIH)=2073.730 E(NOE )=15063.691 E(PLAN)=234.629 | ------------------------------------------------------------------------------- NBONDS: found 14992 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0002 ----------------------- | Etotal =18598.815 grad(E)=48.109 E(BOND)=602.015 E(VDW )=2589.473 | | E(CDIH)=1715.631 E(NOE )=13463.672 E(PLAN)=228.023 | ------------------------------------------------------------------------------- NBONDS: found 14895 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =16570.377 grad(E)=44.831 E(BOND)=540.774 E(VDW )=2233.698 | | E(CDIH)=1609.702 E(NOE )=11970.117 E(PLAN)=216.085 | ------------------------------------------------------------------------------- NBONDS: found 14764 intra-atom interactions NBONDS: found 14661 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =14905.062 grad(E)=44.925 E(BOND)=475.105 E(VDW )=1975.299 | | E(CDIH)=1393.703 E(NOE )=10879.839 E(PLAN)=181.116 | ------------------------------------------------------------------------------- NBONDS: found 14598 intra-atom interactions NBONDS: found 14554 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0001 ----------------------- | Etotal =13206.273 grad(E)=39.501 E(BOND)=354.093 E(VDW )=1626.715 | | E(CDIH)=1201.837 E(NOE )=9861.463 E(PLAN)=162.165 | ------------------------------------------------------------------------------- NBONDS: found 14480 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0002 ----------------------- | Etotal =12200.957 grad(E)=64.019 E(BOND)=344.594 E(VDW )=1163.350 | | E(CDIH)=1338.786 E(NOE )=9211.987 E(PLAN)=142.241 | ------------------------------------------------------------------------------- NBONDS: found 14236 intra-atom interactions NBONDS: found 14396 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0001 ----------------------- | Etotal =11369.419 grad(E)=19.784 E(BOND)=209.801 E(VDW )=999.355 | | E(CDIH)=1063.266 E(NOE )=8961.334 E(PLAN)=135.663 | ------------------------------------------------------------------------------- NBONDS: found 14411 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0002 ----------------------- | Etotal =10734.158 grad(E)=24.533 E(BOND)=236.427 E(VDW )=873.336 | | E(CDIH)=952.312 E(NOE )=8550.921 E(PLAN)=121.161 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =10097.671 grad(E)=23.616 E(BOND)=227.221 E(VDW )=790.907 | | E(CDIH)=803.613 E(NOE )=8175.276 E(PLAN)=100.655 | ------------------------------------------------------------------------------- NBONDS: found 14386 intra-atom interactions --------------- cycle= 160 ------ stepsize= 0.0000 ----------------------- | Etotal =9915.103 grad(E)=19.234 E(BOND)=199.609 E(VDW )=767.615 | | E(CDIH)=767.611 E(NOE )=8087.338 E(PLAN)=92.930 | ------------------------------------------------------------------------------- --------------- cycle= 170 ------ stepsize= 0.0000 ----------------------- | Etotal =9913.738 grad(E)=19.439 E(BOND)=200.125 E(VDW )=767.354 | | E(CDIH)=767.099 E(NOE )=8086.336 E(PLAN)=92.825 | ------------------------------------------------------------------------------- --------------- cycle= 180 ------ stepsize= 0.0000 ----------------------- | Etotal =9913.728 grad(E)=19.441 E(BOND)=200.129 E(VDW )=767.352 | | E(CDIH)=767.095 E(NOE )=8086.328 E(PLAN)=92.824 | ------------------------------------------------------------------------------- --------------- cycle= 190 ------ stepsize= 0.0000 ----------------------- | Etotal =9913.728 grad(E)=19.441 E(BOND)=200.129 E(VDW )=767.352 | | E(CDIH)=767.095 E(NOE )=8086.328 E(PLAN)=92.824 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =9913.728 grad(E)=19.441 E(BOND)=200.129 E(VDW )=767.352 | | E(CDIH)=767.095 E(NOE )=8086.328 E(PLAN)=92.824 | ------------------------------------------------------------------------------- --------------- cycle= 210 ------ stepsize= 0.0000 ----------------------- | Etotal =9913.728 grad(E)=19.441 E(BOND)=200.129 E(VDW )=767.352 | | E(CDIH)=767.095 E(NOE )=8086.328 E(PLAN)=92.824 | ------------------------------------------------------------------------------- --------------- cycle= 220 ------ stepsize= 0.0000 ----------------------- | Etotal =9913.728 grad(E)=19.441 E(BOND)=200.129 E(VDW )=767.352 | | E(CDIH)=767.095 E(NOE )=8086.328 E(PLAN)=92.824 | ------------------------------------------------------------------------------- --------------- cycle= 230 ------ stepsize= 0.0000 ----------------------- | Etotal =9913.728 grad(E)=19.441 E(BOND)=200.129 E(VDW )=767.352 | | E(CDIH)=767.095 E(NOE )=8086.328 E(PLAN)=92.824 | ------------------------------------------------------------------------------- --------------- cycle= 240 ------ stepsize= 0.0000 ----------------------- | Etotal =9913.728 grad(E)=19.441 E(BOND)=200.129 E(VDW )=767.352 | | E(CDIH)=767.095 E(NOE )=8086.328 E(PLAN)=92.824 | ------------------------------------------------------------------------------- --------------- cycle= 250 ------ stepsize= 0.0000 ----------------------- | Etotal =9913.728 grad(E)=19.441 E(BOND)=200.129 E(VDW )=767.352 | | E(CDIH)=767.095 E(NOE )=8086.328 E(PLAN)=92.824 | ------------------------------------------------------------------------------- --------------- cycle= 260 ------ stepsize= 0.0000 ----------------------- | Etotal =9913.728 grad(E)=19.441 E(BOND)=200.129 E(VDW )=767.352 | | E(CDIH)=767.095 E(NOE )=8086.328 E(PLAN)=92.824 | ------------------------------------------------------------------------------- --------------- cycle= 270 ------ stepsize= 0.0000 ----------------------- | Etotal =9913.728 grad(E)=19.441 E(BOND)=200.129 E(VDW )=767.352 | | E(CDIH)=767.095 E(NOE )=8086.328 E(PLAN)=92.824 | ------------------------------------------------------------------------------- --------------- cycle= 280 ------ stepsize= 0.0000 ----------------------- | Etotal =9913.728 grad(E)=19.441 E(BOND)=200.129 E(VDW )=767.352 | | E(CDIH)=767.095 E(NOE )=8086.328 E(PLAN)=92.824 | ------------------------------------------------------------------------------- --------------- cycle= 290 ------ stepsize= 0.0000 ----------------------- | Etotal =9913.728 grad(E)=19.441 E(BOND)=200.129 E(VDW )=767.352 | | E(CDIH)=767.095 E(NOE )=8086.328 E(PLAN)=92.824 | ------------------------------------------------------------------------------- --------------- cycle= 300 ------ stepsize= 0.0000 ----------------------- | Etotal =9913.728 grad(E)=19.441 E(BOND)=200.129 E(VDW )=767.352 | | E(CDIH)=767.095 E(NOE )=8086.328 E(PLAN)=92.824 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination 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 14353 intra-atom interactions NBONDS: found 14325 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =99351.321 grad(E)=332.498 E(BOND)=14395.385 E(ANGL)=68216.737 | | E(VDW )=2988.830 E(CDIH)=1569.430 E(NOE )=11987.185 E(PLAN)=193.754 | ------------------------------------------------------------------------------- NBONDS: found 14312 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =66559.027 grad(E)=156.481 E(BOND)=4160.317 E(ANGL)=39632.848 | | E(VDW )=3815.035 E(CDIH)=2147.908 E(NOE )=16582.338 E(PLAN)=220.580 | ------------------------------------------------------------------------------- NBONDS: found 14286 intra-atom interactions NBONDS: found 14244 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =54174.870 grad(E)=121.387 E(BOND)=2972.595 E(ANGL)=27205.454 | | E(VDW )=4031.764 E(CDIH)=2420.171 E(NOE )=17296.795 E(PLAN)=248.092 | ------------------------------------------------------------------------------- NBONDS: found 14153 intra-atom interactions NBONDS: found 14111 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =48235.555 grad(E)=133.091 E(BOND)=2717.249 E(ANGL)=22537.661 | | E(VDW )=3732.981 E(CDIH)=2687.627 E(NOE )=16295.067 E(PLAN)=264.971 | ------------------------------------------------------------------------------- NBONDS: found 14081 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =43341.356 grad(E)=93.391 E(BOND)=2348.056 E(ANGL)=18911.336 | | E(VDW )=3330.598 E(CDIH)=2745.219 E(NOE )=15707.798 E(PLAN)=298.349 | ------------------------------------------------------------------------------- NBONDS: found 13995 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =40053.523 grad(E)=67.906 E(BOND)=1919.820 E(ANGL)=16972.369 | | E(VDW )=3288.187 E(CDIH)=2719.910 E(NOE )=14854.876 E(PLAN)=298.361 | ------------------------------------------------------------------------------- NBONDS: found 13865 intra-atom interactions NBONDS: found 13834 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =37514.439 grad(E)=85.545 E(BOND)=1730.027 E(ANGL)=15516.566 | | E(VDW )=3137.781 E(CDIH)=2714.125 E(NOE )=14113.139 E(PLAN)=302.802 | ------------------------------------------------------------------------------- NBONDS: found 13750 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =35522.717 grad(E)=58.219 E(BOND)=1405.052 E(ANGL)=14462.794 | | E(VDW )=3075.168 E(CDIH)=2706.004 E(NOE )=13574.021 E(PLAN)=299.678 | ------------------------------------------------------------------------------- NBONDS: found 13690 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =33761.538 grad(E)=51.820 E(BOND)=1303.869 E(ANGL)=13649.114 | | E(VDW )=3028.022 E(CDIH)=2684.031 E(NOE )=12813.740 E(PLAN)=282.762 | ------------------------------------------------------------------------------- NBONDS: found 13591 intra-atom interactions NBONDS: found 13528 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =32320.545 grad(E)=51.216 E(BOND)=1261.486 E(ANGL)=13159.415 | | E(VDW )=2788.694 E(CDIH)=2645.985 E(NOE )=12182.253 E(PLAN)=282.711 | ------------------------------------------------------------------------------- NBONDS: found 13460 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0001 ----------------------- | Etotal =29952.503 grad(E)=65.307 E(BOND)=1291.613 E(ANGL)=11352.441 | | E(VDW )=2595.022 E(CDIH)=2597.687 E(NOE )=11830.308 E(PLAN)=285.431 | ------------------------------------------------------------------------------- NBONDS: found 13403 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0001 ----------------------- | Etotal =28629.541 grad(E)=42.668 E(BOND)=1130.219 E(ANGL)=10740.378 | | E(VDW )=2417.549 E(CDIH)=2593.394 E(NOE )=11452.337 E(PLAN)=295.664 | ------------------------------------------------------------------------------- NBONDS: found 13289 intra-atom interactions NBONDS: found 13185 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0001 ----------------------- | Etotal =27408.601 grad(E)=50.348 E(BOND)=1088.750 E(ANGL)=10451.891 | | E(VDW )=2030.187 E(CDIH)=2612.192 E(NOE )=10904.914 E(PLAN)=320.667 | ------------------------------------------------------------------------------- NBONDS: found 13063 intra-atom interactions NBONDS: found 13022 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0001 ----------------------- | Etotal =24924.418 grad(E)=57.835 E(BOND)=1151.520 E(ANGL)=8486.640 | | E(VDW )=1812.552 E(CDIH)=2636.311 E(NOE )=10492.535 E(PLAN)=344.861 | ------------------------------------------------------------------------------- NBONDS: found 12980 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =23394.173 grad(E)=44.975 E(BOND)=1027.319 E(ANGL)=7861.903 | | E(VDW )=1587.835 E(CDIH)=2598.865 E(NOE )=9973.767 E(PLAN)=344.484 | ------------------------------------------------------------------------------- NBONDS: found 12930 intra-atom interactions --------------- cycle= 160 ------ stepsize= 0.0001 ----------------------- | Etotal =22208.328 grad(E)=38.422 E(BOND)=899.158 E(ANGL)=7636.818 | | E(VDW )=1360.677 E(CDIH)=2601.859 E(NOE )=9380.264 E(PLAN)=329.551 | ------------------------------------------------------------------------------- NBONDS: found 12809 intra-atom interactions --------------- cycle= 170 ------ stepsize= 0.0001 ----------------------- | Etotal =21214.294 grad(E)=40.029 E(BOND)=850.934 E(ANGL)=7221.245 | | E(VDW )=1361.298 E(CDIH)=2599.546 E(NOE )=8872.635 E(PLAN)=308.637 | ------------------------------------------------------------------------------- NBONDS: found 12690 intra-atom interactions --------------- cycle= 180 ------ stepsize= 0.0001 ----------------------- | Etotal =20179.493 grad(E)=39.395 E(BOND)=799.682 E(ANGL)=6716.056 | | E(VDW )=1350.253 E(CDIH)=2594.093 E(NOE )=8411.825 E(PLAN)=307.584 | ------------------------------------------------------------------------------- NBONDS: found 12600 intra-atom interactions --------------- cycle= 190 ------ stepsize= 0.0001 ----------------------- | Etotal =19415.905 grad(E)=34.130 E(BOND)=803.010 E(ANGL)=6289.620 | | E(VDW )=1311.163 E(CDIH)=2592.075 E(NOE )=8090.507 E(PLAN)=329.530 | ------------------------------------------------------------------------------- NBONDS: found 12558 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =18848.695 grad(E)=25.855 E(BOND)=778.024 E(ANGL)=5852.276 | | E(VDW )=1323.195 E(CDIH)=2628.782 E(NOE )=7909.091 E(PLAN)=357.327 | ------------------------------------------------------------------------------- NBONDS: found 12497 intra-atom interactions NBONDS: found 12409 intra-atom interactions --------------- cycle= 210 ------ stepsize= 0.0001 ----------------------- | Etotal =18404.743 grad(E)=22.582 E(BOND)=761.449 E(ANGL)=5422.998 | | E(VDW )=1324.951 E(CDIH)=2687.563 E(NOE )=7834.399 E(PLAN)=373.382 | ------------------------------------------------------------------------------- NBONDS: found 12356 intra-atom interactions --------------- cycle= 220 ------ stepsize= 0.0001 ----------------------- | Etotal =17975.258 grad(E)=29.115 E(BOND)=748.360 E(ANGL)=5075.215 | | E(VDW )=1295.958 E(CDIH)=2695.258 E(NOE )=7783.778 E(PLAN)=376.690 | ------------------------------------------------------------------------------- NBONDS: found 12285 intra-atom interactions --------------- cycle= 230 ------ stepsize= 0.0001 ----------------------- | Etotal =17420.647 grad(E)=29.995 E(BOND)=724.219 E(ANGL)=4821.357 | | E(VDW )=1202.957 E(CDIH)=2642.327 E(NOE )=7662.843 E(PLAN)=366.944 | ------------------------------------------------------------------------------- --------------- cycle= 240 ------ stepsize= 0.0001 ----------------------- | Etotal =17012.280 grad(E)=25.595 E(BOND)=701.911 E(ANGL)=4670.286 | | E(VDW )=1154.187 E(CDIH)=2584.385 E(NOE )=7548.582 E(PLAN)=352.929 | ------------------------------------------------------------------------------- NBONDS: found 12212 intra-atom interactions NBONDS: found 12125 intra-atom interactions --------------- cycle= 250 ------ stepsize= 0.0001 ----------------------- | Etotal =16670.751 grad(E)=23.963 E(BOND)=693.176 E(ANGL)=4529.010 | | E(VDW )=1131.754 E(CDIH)=2576.586 E(NOE )=7404.596 E(PLAN)=335.629 | ------------------------------------------------------------------------------- NBONDS: found 12072 intra-atom interactions --------------- cycle= 260 ------ stepsize= 0.0001 ----------------------- | Etotal =16388.812 grad(E)=20.714 E(BOND)=692.919 E(ANGL)=4464.991 | | E(VDW )=1120.533 E(CDIH)=2583.230 E(NOE )=7210.632 E(PLAN)=316.506 | ------------------------------------------------------------------------------- NBONDS: found 12016 intra-atom interactions --------------- cycle= 270 ------ stepsize= 0.0001 ----------------------- | Etotal =16140.778 grad(E)=24.328 E(BOND)=684.053 E(ANGL)=4389.008 | | E(VDW )=1110.682 E(CDIH)=2554.178 E(NOE )=7104.137 E(PLAN)=298.721 | ------------------------------------------------------------------------------- NBONDS: found 11980 intra-atom interactions --------------- cycle= 280 ------ stepsize= 0.0001 ----------------------- | Etotal =15876.898 grad(E)=22.190 E(BOND)=662.456 E(ANGL)=4304.626 | | E(VDW )=1097.439 E(CDIH)=2532.752 E(NOE )=6986.325 E(PLAN)=293.301 | ------------------------------------------------------------------------------- NBONDS: found 11947 intra-atom interactions --------------- cycle= 290 ------ stepsize= 0.0001 ----------------------- | Etotal =15619.280 grad(E)=19.900 E(BOND)=637.559 E(ANGL)=4279.166 | | E(VDW )=1078.749 E(CDIH)=2497.987 E(NOE )=6832.003 E(PLAN)=293.816 | ------------------------------------------------------------------------------- --------------- cycle= 300 ------ stepsize= 0.0001 ----------------------- | Etotal =15408.475 grad(E)=18.093 E(BOND)=635.279 E(ANGL)=4268.800 | | E(VDW )=1060.966 E(CDIH)=2474.010 E(NOE )=6674.511 E(PLAN)=294.908 | ------------------------------------------------------------------------------- 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= 0.158400140E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : -0.00001 0.00001 0.00001 velocity [A/ps] : -0.08740 0.10192 0.17449 ang. mom. [amu A/ps] :-163037.56023 -18647.76195 -86420.42238 kin. ener. [Kcal/mol] : 3.92149 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : -0.00001 0.00001 0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 CODIMP: improper type-based parameters retrieved NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 728 exclusions and 0 interactions(1-4) NBONDS: found 11906 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=24947.689 E(kin)=6320.695 temperature=3132.170 | | Etotal =18626.994 grad(E)=81.420 E(BOND)=63.528 E(ANGL)=426.880 | | E(DIHE)=0.000 E(IMPR)=7632.190 E(VDW )=1060.966 E(CDIH)=2474.010 | | E(NOE )=6674.511 E(PLAN)=294.908 | ------------------------------------------------------------------------------- NBONDS: found 11918 intra-atom interactions NBONDS: found 11918 intra-atom interactions NBONDS: found 11847 intra-atom interactions NBONDS: found 11795 intra-atom interactions NBONDS: found 11742 intra-atom interactions NBONDS: found 11686 intra-atom interactions NBONDS: found 11645 intra-atom interactions NBONDS: found 11615 intra-atom interactions NBONDS: found 11519 intra-atom interactions NBONDS: found 11456 intra-atom interactions NBONDS: found 11418 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=23367.046 E(kin)=6667.699 temperature=3304.125 | | Etotal =16699.347 grad(E)=68.073 E(BOND)=2642.517 E(ANGL)=4679.708 | | E(DIHE)=0.000 E(IMPR)=3598.923 E(VDW )=364.644 E(CDIH)=1356.112 | | E(NOE )=3796.155 E(PLAN)=261.288 | ------------------------------------------------------------------------------- NBONDS: found 11370 intra-atom interactions NBONDS: found 11344 intra-atom interactions NBONDS: found 11285 intra-atom interactions NBONDS: found 11165 intra-atom interactions NBONDS: found 11097 intra-atom interactions NBONDS: found 11013 intra-atom interactions NBONDS: found 10963 intra-atom interactions NBONDS: found 10942 intra-atom interactions NBONDS: found 10893 intra-atom interactions NBONDS: found 10907 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=21347.609 E(kin)=6516.698 temperature=3229.297 | | Etotal =14830.911 grad(E)=67.406 E(BOND)=2392.987 E(ANGL)=4396.962 | | E(DIHE)=0.000 E(IMPR)=2832.311 E(VDW )=378.054 E(CDIH)=1398.807 | | E(NOE )=3281.753 E(PLAN)=150.036 | ------------------------------------------------------------------------------- NBONDS: found 10906 intra-atom interactions NBONDS: found 10876 intra-atom interactions NBONDS: found 10862 intra-atom interactions NBONDS: found 10866 intra-atom interactions NBONDS: found 10850 intra-atom interactions NBONDS: found 10808 intra-atom interactions NBONDS: found 10818 intra-atom interactions NBONDS: found 10794 intra-atom interactions NBONDS: found 10778 intra-atom interactions NBONDS: found 10788 intra-atom interactions NBONDS: found 10789 intra-atom interactions NBONDS: found 10794 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=19365.847 E(kin)=6746.981 temperature=3343.412 | | Etotal =12618.866 grad(E)=62.918 E(BOND)=2078.674 E(ANGL)=3776.641 | | E(DIHE)=0.000 E(IMPR)=2524.235 E(VDW )=247.058 E(CDIH)=699.013 | | E(NOE )=3110.699 E(PLAN)=182.546 | ------------------------------------------------------------------------------- NBONDS: found 10825 intra-atom interactions NBONDS: found 10880 intra-atom interactions NBONDS: found 10941 intra-atom interactions NBONDS: found 10936 intra-atom interactions NBONDS: found 10944 intra-atom interactions NBONDS: found 10945 intra-atom interactions NBONDS: found 10924 intra-atom interactions NBONDS: found 10915 intra-atom interactions NBONDS: found 10921 intra-atom interactions NBONDS: found 10950 intra-atom interactions NBONDS: found 10940 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=18237.490 E(kin)=6502.851 temperature=3222.436 | | Etotal =11734.639 grad(E)=66.133 E(BOND)=2126.582 E(ANGL)=3251.650 | | E(DIHE)=0.000 E(IMPR)=2114.217 E(VDW )=427.483 E(CDIH)=453.191 | | E(NOE )=3206.615 E(PLAN)=154.900 | ------------------------------------------------------------------------------- NBONDS: found 10929 intra-atom interactions NBONDS: found 10929 intra-atom interactions NBONDS: found 10906 intra-atom interactions NBONDS: found 10899 intra-atom interactions NBONDS: found 10868 intra-atom interactions NBONDS: found 10883 intra-atom interactions NBONDS: found 10827 intra-atom interactions NBONDS: found 10808 intra-atom interactions NBONDS: found 10861 intra-atom interactions NBONDS: found 10860 intra-atom interactions NBONDS: found 10854 intra-atom interactions NBONDS: found 10856 intra-atom interactions NBONDS: found 10847 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=17459.197 E(kin)=6080.385 temperature=3013.086 | | Etotal =11378.812 grad(E)=64.745 E(BOND)=2231.252 E(ANGL)=3255.327 | | E(DIHE)=0.000 E(IMPR)=2125.421 E(VDW )=305.715 E(CDIH)=365.306 | | E(NOE )=2954.517 E(PLAN)=141.273 | ------------------------------------------------------------------------------- NBONDS: found 10811 intra-atom interactions NBONDS: found 10768 intra-atom interactions NBONDS: found 10702 intra-atom interactions NBONDS: found 10728 intra-atom interactions NBONDS: found 10738 intra-atom interactions NBONDS: found 10718 intra-atom interactions NBONDS: found 10703 intra-atom interactions NBONDS: found 10721 intra-atom interactio