X-PLOR: V3.840 user: on: Alpha/OSF at: 16-Aug-96 17:31:21 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=112924.379882812 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 17:24:34 created by user: COOR>ATOM 1 P GUA 1 12.388 6.391 7.044 1.00 0.00 A COOR>ATOM 2 O1P GUA 1 14.128 6.272 5.783 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 = 2.2782 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.7622 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1390 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2726 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2235 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2887 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6855 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.1921 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.2552 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6244 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.5391 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.9640 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.4981 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.9582 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.4580 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.4888 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9258 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1692 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.7955 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0425 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.8154 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 14544 intra-atom interactions NBONDS: found 14620 intra-atom interactions NBONDS: found 14776 intra-atom interactions NBONDS: found 14871 intra-atom interactions NBONDS: found 15109 intra-atom interactions NBONDS: found 15248 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0002 ----------------------- | Etotal =113786.828 grad(E)=346.265 E(BOND)=15713.433 E(VDW )=9765.032 | | E(CDIH)=4739.871 E(NOE )=82991.787 E(PLAN)=576.705 | ------------------------------------------------------------------------------- NBONDS: found 15363 intra-atom interactions NBONDS: found 15442 intra-atom interactions NBONDS: found 15444 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =66600.478 grad(E)=171.309 E(BOND)=4443.752 E(VDW )=7290.056 | | E(CDIH)=3742.792 E(NOE )=50717.174 E(PLAN)=406.705 | ------------------------------------------------------------------------------- NBONDS: found 15449 intra-atom interactions NBONDS: found 15516 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0002 ----------------------- | Etotal =48759.810 grad(E)=146.290 E(BOND)=2962.549 E(VDW )=4883.893 | | E(CDIH)=3297.464 E(NOE )=37405.403 E(PLAN)=210.501 | ------------------------------------------------------------------------------- NBONDS: found 15489 intra-atom interactions NBONDS: found 15488 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =39098.204 grad(E)=83.514 E(BOND)=1653.431 E(VDW )=4440.165 | | E(CDIH)=2874.056 E(NOE )=29940.573 E(PLAN)=189.978 | ------------------------------------------------------------------------------- NBONDS: found 15520 intra-atom interactions NBONDS: found 15478 intra-atom interactions NBONDS: found 15398 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0002 ----------------------- | Etotal =30775.963 grad(E)=94.339 E(BOND)=1719.265 E(VDW )=3416.713 | | E(CDIH)=2381.032 E(NOE )=23000.528 E(PLAN)=258.425 | ------------------------------------------------------------------------------- NBONDS: found 15310 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0002 ----------------------- | Etotal =25146.833 grad(E)=74.428 E(BOND)=908.944 E(VDW )=2778.481 | | E(CDIH)=2122.318 E(NOE )=19017.733 E(PLAN)=319.356 | ------------------------------------------------------------------------------- --------------- cycle= 70 ------ stepsize= 0.0000 ----------------------- | Etotal =24437.622 grad(E)=77.265 E(BOND)=797.781 E(VDW )=2639.579 | | E(CDIH)=2295.075 E(NOE )=18383.840 E(PLAN)=321.348 | ------------------------------------------------------------------------------- --------------- cycle= 80 ------ stepsize= 0.0000 ----------------------- | Etotal =24437.316 grad(E)=77.278 E(BOND)=797.964 E(VDW )=2639.514 | | E(CDIH)=2295.046 E(NOE )=18383.443 E(PLAN)=321.349 | ------------------------------------------------------------------------------- --------------- cycle= 90 ------ stepsize= 0.0000 ----------------------- | Etotal =24437.313 grad(E)=77.278 E(BOND)=797.966 E(VDW )=2639.513 | | E(CDIH)=2295.045 E(NOE )=18383.440 E(PLAN)=321.349 | ------------------------------------------------------------------------------- %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 15271 intra-atom interactions NBONDS: found 15242 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =121132.312 grad(E)=381.572 E(BOND)=15217.805 E(ANGL)=74692.289 | | E(VDW )=3430.133 E(CDIH)=3938.371 E(NOE )=23278.473 E(PLAN)=575.240 | ------------------------------------------------------------------------------- NBONDS: found 15155 intra-atom interactions NBONDS: found 15031 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =85847.226 grad(E)=161.478 E(BOND)=5349.909 E(ANGL)=44647.356 | | E(VDW )=3814.700 E(CDIH)=4258.200 E(NOE )=27218.463 E(PLAN)=558.600 | ------------------------------------------------------------------------------- NBONDS: found 14961 intra-atom interactions NBONDS: found 14861 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =72920.989 grad(E)=124.190 E(BOND)=3408.171 E(ANGL)=31432.904 | | E(VDW )=3847.925 E(CDIH)=4298.152 E(NOE )=29335.409 E(PLAN)=598.429 | ------------------------------------------------------------------------------- NBONDS: found 14797 intra-atom interactions NBONDS: found 14772 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =63954.125 grad(E)=115.091 E(BOND)=3378.931 E(ANGL)=24704.956 | | E(VDW )=3262.801 E(CDIH)=4247.901 E(NOE )=27778.965 E(PLAN)=580.570 | ------------------------------------------------------------------------------- NBONDS: found 14670 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =58256.920 grad(E)=95.087 E(BOND)=2806.694 E(ANGL)=21140.848 | | E(VDW )=2761.541 E(CDIH)=4439.848 E(NOE )=26526.295 E(PLAN)=581.693 | ------------------------------------------------------------------------------- NBONDS: found 14577 intra-atom interactions NBONDS: found 14465 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =53506.881 grad(E)=70.710 E(BOND)=2382.434 E(ANGL)=18832.459 | | E(VDW )=2285.166 E(CDIH)=4540.447 E(NOE )=24902.564 E(PLAN)=563.812 | ------------------------------------------------------------------------------- NBONDS: found 14382 intra-atom interactions NBONDS: found 14277 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =50535.620 grad(E)=69.082 E(BOND)=2418.756 E(ANGL)=17278.498 | | E(VDW )=2034.843 E(CDIH)=4461.085 E(NOE )=23808.147 E(PLAN)=534.292 | ------------------------------------------------------------------------------- NBONDS: found 14156 intra-atom interactions NBONDS: found 14061 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =47108.127 grad(E)=67.163 E(BOND)=2302.315 E(ANGL)=14803.208 | | E(VDW )=1929.705 E(CDIH)=4327.737 E(NOE )=23255.413 E(PLAN)=489.750 | ------------------------------------------------------------------------------- NBONDS: found 14011 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =43742.962 grad(E)=63.151 E(BOND)=2304.366 E(ANGL)=11980.854 | | E(VDW )=1793.107 E(CDIH)=4168.603 E(NOE )=23027.380 E(PLAN)=468.652 | ------------------------------------------------------------------------------- NBONDS: found 13987 intra-atom interactions NBONDS: found 13937 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =41425.458 grad(E)=53.146 E(BOND)=1960.016 E(ANGL)=10334.568 | | E(VDW )=1697.964 E(CDIH)=4025.636 E(NOE )=22942.382 E(PLAN)=464.893 | ------------------------------------------------------------------------------- --------------- cycle= 110 ------ stepsize= 0.0001 ----------------------- | Etotal =39987.658 grad(E)=50.613 E(BOND)=1835.707 E(ANGL)=9880.445 | | E(VDW )=1532.024 E(CDIH)=3941.752 E(NOE )=22339.463 E(PLAN)=458.267 | ------------------------------------------------------------------------------- NBONDS: found 13865 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0001 ----------------------- | Etotal =38802.775 grad(E)=38.419 E(BOND)=1568.100 E(ANGL)=9361.435 | | E(VDW )=1495.618 E(CDIH)=3789.227 E(NOE )=22137.049 E(PLAN)=451.346 | ------------------------------------------------------------------------------- NBONDS: found 13734 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0001 ----------------------- | Etotal =37607.119 grad(E)=44.571 E(BOND)=1481.574 E(ANGL)=8557.432 | | E(VDW )=1445.704 E(CDIH)=3700.725 E(NOE )=21988.230 E(PLAN)=433.454 | ------------------------------------------------------------------------------- NBONDS: found 13600 intra-atom interactions NBONDS: found 13449 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0001 ----------------------- | Etotal =36396.165 grad(E)=47.001 E(BOND)=1458.045 E(ANGL)=8231.463 | | E(VDW )=1378.805 E(CDIH)=3587.739 E(NOE )=21332.395 E(PLAN)=407.718 | ------------------------------------------------------------------------------- NBONDS: found 13315 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =35527.420 grad(E)=43.015 E(BOND)=1375.164 E(ANGL)=8231.520 | | E(VDW )=1343.454 E(CDIH)=3414.066 E(NOE )=20775.423 E(PLAN)=387.794 | ------------------------------------------------------------------------------- NBONDS: found 13231 intra-atom interactions --------------- cycle= 160 ------ stepsize= 0.0001 ----------------------- | Etotal =33996.170 grad(E)=50.994 E(BOND)=1349.182 E(ANGL)=7848.396 | | E(VDW )=1158.252 E(CDIH)=3292.102 E(NOE )=19995.172 E(PLAN)=353.066 | ------------------------------------------------------------------------------- NBONDS: found 13166 intra-atom interactions NBONDS: found 13078 intra-atom interactions --------------- cycle= 170 ------ stepsize= 0.0001 ----------------------- | Etotal =32709.532 grad(E)=40.807 E(BOND)=1290.027 E(ANGL)=7358.119 | | E(VDW )=1108.710 E(CDIH)=3120.116 E(NOE )=19504.524 E(PLAN)=328.036 | ------------------------------------------------------------------------------- NBONDS: found 13014 intra-atom interactions --------------- cycle= 180 ------ stepsize= 0.0001 ----------------------- | Etotal =32073.018 grad(E)=37.789 E(BOND)=1257.163 E(ANGL)=7360.229 | | E(VDW )=1049.299 E(CDIH)=3004.677 E(NOE )=19091.123 E(PLAN)=310.527 | ------------------------------------------------------------------------------- NBONDS: found 12947 intra-atom interactions --------------- cycle= 190 ------ stepsize= 0.0001 ----------------------- | Etotal =31542.005 grad(E)=25.743 E(BOND)=1235.505 E(ANGL)=7185.156 | | E(VDW )=967.068 E(CDIH)=2968.024 E(NOE )=18890.158 E(PLAN)=296.095 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =30892.941 grad(E)=26.363 E(BOND)=1197.760 E(ANGL)=6907.969 | | E(VDW )=906.348 E(CDIH)=2925.947 E(NOE )=18664.752 E(PLAN)=290.165 | ------------------------------------------------------------------------------- NBONDS: found 12915 intra-atom interactions --------------- cycle= 210 ------ stepsize= 0.0001 ----------------------- | Etotal =30412.251 grad(E)=24.332 E(BOND)=1169.083 E(ANGL)=6822.827 | | E(VDW )=845.217 E(CDIH)=2883.057 E(NOE )=18406.111 E(PLAN)=285.955 | ------------------------------------------------------------------------------- NBONDS: found 12845 intra-atom interactions --------------- cycle= 220 ------ stepsize= 0.0001 ----------------------- | Etotal =29992.512 grad(E)=28.433 E(BOND)=1110.142 E(ANGL)=6721.353 | | E(VDW )=774.117 E(CDIH)=2857.009 E(NOE )=18243.897 E(PLAN)=285.995 | ------------------------------------------------------------------------------- --------------- cycle= 230 ------ stepsize= 0.0001 ----------------------- | Etotal =29580.220 grad(E)=26.551 E(BOND)=1059.030 E(ANGL)=6627.589 | | E(VDW )=733.386 E(CDIH)=2830.403 E(NOE )=18040.875 E(PLAN)=288.936 | ------------------------------------------------------------------------------- NBONDS: found 12762 intra-atom interactions --------------- cycle= 240 ------ stepsize= 0.0001 ----------------------- | Etotal =29289.500 grad(E)=20.932 E(BOND)=1027.662 E(ANGL)=6581.480 | | E(VDW )=690.296 E(CDIH)=2802.867 E(NOE )=17904.010 E(PLAN)=283.186 | ------------------------------------------------------------------------------- NBONDS: found 12677 intra-atom interactions --------------- cycle= 250 ------ stepsize= 0.0001 ----------------------- | Etotal =28987.063 grad(E)=24.421 E(BOND)=1065.636 E(ANGL)=6438.919 | | E(VDW )=652.915 E(CDIH)=2778.226 E(NOE )=17772.161 E(PLAN)=279.206 | ------------------------------------------------------------------------------- NBONDS: found 12594 intra-atom interactions --------------- cycle= 260 ------ stepsize= 0.0001 ----------------------- | Etotal =28683.415 grad(E)=19.319 E(BOND)=1015.719 E(ANGL)=6250.982 | | E(VDW )=644.973 E(CDIH)=2756.701 E(NOE )=17732.638 E(PLAN)=282.401 | ------------------------------------------------------------------------------- NBONDS: found 12571 intra-atom interactions --------------- cycle= 270 ------ stepsize= 0.0001 ----------------------- | Etotal =28485.143 grad(E)=15.714 E(BOND)=1006.963 E(ANGL)=6199.483 | | E(VDW )=622.829 E(CDIH)=2743.562 E(NOE )=17623.859 E(PLAN)=288.447 | ------------------------------------------------------------------------------- NBONDS: found 12528 intra-atom interactions --------------- cycle= 280 ------ stepsize= 0.0001 ----------------------- | Etotal =28318.265 grad(E)=16.152 E(BOND)=953.733 E(ANGL)=6229.151 | | E(VDW )=596.258 E(CDIH)=2741.818 E(NOE )=17500.510 E(PLAN)=296.795 | ------------------------------------------------------------------------------- NBONDS: found 12521 intra-atom interactions --------------- cycle= 290 ------ stepsize= 0.0001 ----------------------- | Etotal =28182.985 grad(E)=13.671 E(BOND)=952.094 E(ANGL)=6225.825 | | E(VDW )=586.214 E(CDIH)=2735.876 E(NOE )=17385.330 E(PLAN)=297.646 | ------------------------------------------------------------------------------- --------------- cycle= 300 ------ stepsize= 0.0001 ----------------------- | Etotal =28026.197 grad(E)=16.806 E(BOND)=918.129 E(ANGL)=6185.477 | | E(VDW )=592.979 E(CDIH)=2711.588 E(NOE )=17322.886 E(PLAN)=295.138 | ------------------------------------------------------------------------------- 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= 0.169960960E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 0.00001 -0.00002 0.00000 velocity [A/ps] : -0.13311 -0.17253 0.07334 ang. mom. [amu A/ps] : -1697.46564 -72768.54987 56845.09300 kin. ener. [Kcal/mol] : 4.27678 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00001 -0.00002 0.00000 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 12516 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=36792.099 E(kin)=6052.473 temperature=2999.255 | | Etotal =30739.626 grad(E)=85.524 E(BOND)=91.813 E(ANGL)=618.548 | | E(DIHE)=0.000 E(IMPR)=9106.674 E(VDW )=592.979 E(CDIH)=2711.588 | | E(NOE )=17322.886 E(PLAN)=295.138 | ------------------------------------------------------------------------------- NBONDS: found 12515 intra-atom interactions NBONDS: found 12521 intra-atom interactions NBONDS: found 12514 intra-atom interactions NBONDS: found 12553 intra-atom interactions NBONDS: found 12516 intra-atom interactions NBONDS: found 12506 intra-atom interactions NBONDS: found 12496 intra-atom interactions NBONDS: found 12521 intra-atom interactions NBONDS: found 12545 intra-atom interactions NBONDS: found 12538 intra-atom interactions NBONDS: found 12518 intra-atom interactions NBONDS: found 12522 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=33423.021 E(kin)=6926.855 temperature=3432.547 | | Etotal =26496.167 grad(E)=68.873 E(BOND)=3145.076 E(ANGL)=4818.770 | | E(DIHE)=0.000 E(IMPR)=4956.889 E(VDW )=538.177 E(CDIH)=2129.067 | | E(NOE )=10654.683 E(PLAN)=253.505 | ------------------------------------------------------------------------------- NBONDS: found 12483 intra-atom interactions NBONDS: found 12524 intra-atom interactions NBONDS: found 12495 intra-atom interactions NBONDS: found 12441 intra-atom interactions NBONDS: found 12427 intra-atom interactions NBONDS: found 12411 intra-atom interactions NBONDS: found 12398 intra-atom interactions NBONDS: found 12417 intra-atom interactions NBONDS: found 12299 intra-atom interactions NBONDS: found 12203 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=31484.459 E(kin)=6235.586 temperature=3089.995 | | Etotal =25248.873 grad(E)=69.690 E(BOND)=2861.870 E(ANGL)=5319.820 | | E(DIHE)=0.000 E(IMPR)=4360.881 E(VDW )=423.940 E(CDIH)=1855.207 | | E(NOE )=10210.115 E(PLAN)=217.039 | ------------------------------------------------------------------------------- NBONDS: found 12157 intra-atom interactions NBONDS: found 12076 intra-atom interactions NBONDS: found 12021 intra-atom interactions NBONDS: found 11942 intra-atom interactions NBONDS: found 11941 intra-atom interactions NBONDS: found 11923 intra-atom interactions NBONDS: found 11891 intra-atom interactions NBONDS: found 11872 intra-atom interactions NBONDS: found 11861 intra-atom interactions NBONDS: found 11819 intra-atom interactions NBONDS: found 11796 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=30398.361 E(kin)=6598.491 temperature=3269.830 | | Etotal =23799.869 grad(E)=66.380 E(BOND)=2644.543 E(ANGL)=5013.353 | | E(DIHE)=0.000 E(IMPR)=4139.544 E(VDW )=520.692 E(CDIH)=1393.894 | | E(NOE )=9942.031 E(PLAN)=145.812 | ------------------------------------------------------------------------------- NBONDS: found 11768 intra-atom interactions NBONDS: found 11739 intra-atom interactions NBONDS: found 11770 intra-atom interactions NBONDS: found 11785 intra-atom interactions NBONDS: found 11809 intra-atom interactions NBONDS: found 11823 intra-atom interactions NBONDS: found 11827 intra-atom interactions NBONDS: found 11835 intra-atom interactions NBONDS: found 11866 intra-atom interactions NBONDS: found 11855 intra-atom interactions NBONDS: found 11815 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=28834.551 E(kin)=6810.501 temperature=3374.889 | | Etotal =22024.050 grad(E)=64.674 E(BOND)=2438.513 E(ANGL)=4654.042 | | E(DIHE)=0.000 E(IMPR)=4239.386 E(VDW )=361.654 E(CDIH)=1395.286 | | E(NOE )=8742.968 E(PLAN)=192.201 | ------------------------------------------------------------------------------- NBONDS: found 11815 intra-atom interactions NBONDS: found 11817 intra-atom interactions NBONDS: found 11814 intra-atom interactions NBONDS: found 11849 intra-atom interactions NBONDS: found 11846 intra-atom interactions NBONDS: found 11858 intra-atom interactions NBONDS: found 11896 intra-atom interactions NBONDS: found 11887 intra-atom interactions NBONDS: found 11895 intra-atom interactions NBONDS: found 11947 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=27342.256 E(kin)=6411.213 temperature=3177.025 | | Etotal =20931.043 grad(E)=64.957 E(BOND)=2539.739 E(ANGL)=4153.039 | | E(DIHE)=0.000 E(IMPR)=4016.096 E(VDW )=373.623 E(CDIH)=1493.394 | | E(NOE )=8232.850 E(PLAN)=122.302 | ------------------------------------------------------------------------------- NBONDS: found 11955 intra-atom interactions NBONDS: found 11946 intra-atom interactions NBONDS: found 11978 intra-atom interactions NBONDS: found 11919 intra-atom interactions NBONDS: found 11940 intra-atom interactions NBONDS: found 11908 intra-atom interactions NBONDS: found 11928 intra-atom interactions NBONDS: found 11932 intra-atom interactions NBONDS: found 11926 intra-atom interactions NBONDS: found 11909 intra-atom interactions NBONDS: found 11934 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=25944.942 E(kin)=6174.553 temperature=3059.750 | | Etotal =19770.389 grad(E)=62.604 E(BOND)=2310.937 E(ANGL)=4228.085 | | E(DIHE)=0.000 E(IMPR)=4042.589 E(VDW )=516.672 E(CDIH)=1516.722 | | E(NOE )=6958.011 E(PLAN)=197.372 | ------------------------------------------------------------------------------- NBONDS: found 11938 intra-atom interactions NBONDS: found 11928 intra-atom interactions NBONDS: found 11909 intra-atom interactions NBONDS: found 11927 intra-atom interactions NBONDS: found 11902 intra-atom interactions NBONDS: found 11896 intra-atom interactions NBONDS: found 11923 intra-atom interactions NBONDS: found 11937 intra-atom interactions NBONDS: found 11944 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=25457.904 E(kin)=6111.936 temperature=3028.721 | | Etotal =19345.969 grad(E)=61.223 E(BOND)=2417.811 E(ANGL)=4029.865 | | E(DIHE)=0.000 E(IMPR)=3845.678 E(VDW )=442.988 E(CDIH)=1540.370 | | E(NOE )=6917.104 E(PLAN)=152.153 | ------------------------------------------------------------------------------- NBONDS: found 11937 intra-atom interactions NBONDS: found 11926 intra-atom interactions NBONDS: found 11948 intra-atom interactions NBONDS: found 12007 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00001 -0.00002 0.00000 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 -0.00002 0.00000 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 -0.00002 0.00000 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 12030 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=35724.674 E(kin)=6045.800 temperature=2995.948 | | Etotal =29678.874 grad(E)=119.198 E(BOND)=4881.594 E(ANGL)=8527.676 | | E(DIHE)=0.000 E(IMPR)=7352.107 E(VDW )=396.654 E(CDIH)=1671.101 | | E(NOE )=6720.478 E(PLAN)=129.265 | ------------------------------------------------------------------------------- NBONDS: found 12091 intra-atom interactions NBONDS: found 12138 intra-atom interactions NBONDS: found 12127 intra-atom interactions NBONDS: found 12142 intra-atom interactions NBONDS: found 12105 intra-atom interactions NBONDS: found 12114 intra-atom interactions NBONDS: found 12112 intra-atom interactions NBONDS: found 12131 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=31864.517 E(kin)=6595.094 temperature=3268.146 | | Etotal =25269.423 grad(E)=87.704 E(BOND)=2864.086 E(ANGL)=5775.349 | | E(DIHE)=0.000 E(IMPR)=6059.252 E(VDW )=672.675 E(CDIH)=1999.509 | | E(NOE )=7650.556 E(PLAN)=247.995 | ------------------------------------------------------------------------------- NBONDS: found 12125 intra-atom interactions NBONDS: found 12118 intra-atom interactions NBONDS: found 12192 intra-atom interactions NBONDS: found 12209 intra-atom interactions NBONDS: found 12224 intra-atom interactions NBONDS: found 12261 intra-atom interactions NBONDS: found 12276 intra-atom interactions NBONDS: found 12282 intra-atom interactions NBONDS: found 12282 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=30843.821 E(kin)=5876.832 temperature=2912.217 | | Etotal =24966.988 grad(E)=88.459 E(BOND)=2755.903 E(ANGL)=5516.835 | | E(DIHE)=0.000 E(IMPR)=5938.360 E(VDW )=640.857 E(CDIH)=1878.338 | | E(NOE )=7939.840 E(PLAN)=296.854 | ------------------------------------------------------------------------------- NBONDS: found 12332 intra-atom interactions NBONDS: found 12295 intra-atom interactions NBONDS: found 12286 intra-atom interactions NBONDS: found 12300 intra-atom interactions NBONDS: found 12289 intra-atom interactions NBONDS: found 12250 intra-atom interactions NBONDS: found 12242 intra-atom interactions NBONDS: found 12287 intra-atom interactions NBONDS: found 12316 intra-atom interactions NBONDS: found 12296 intra-atom interactions NBONDS: found 12354 intra-atom interactions NBONDS: found 12340 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=30636.679 E(kin)=6437.786 temperature=3190.193 | | Etotal =24198.893 grad(E)=88.199 E(BOND)=2845.177 E(ANGL)=5399.529 | | E(DIHE)=0.000 E(IMPR)=5829.725 E(VDW )=656.802 E(CDIH)=1972.796 | | E(NOE )=7313.489 E(PLAN)=181.375 | ------------------------------------------------------------------------------- NBONDS: found 12409 intra-atom interactions NBONDS: found 12427 intra-atom interactions NBONDS: found 12454 intra-atom interactions NBONDS: found 12453 intra-atom interactions NBONDS: found 12456 intra-atom interactions NBONDS: found 12448 intra-atom interactions NBONDS: found 12449 intra-atom interactions NBONDS: found 12436 intra-atom interactions NBONDS: found 12425 intra-atom interactions NBONDS: found 12446 intra-atom interactions NBONDS: found 12419 intra-atom interactions NBONDS: found 12426 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=29707.393 E(kin)=6363.509 temperature=3153.386 | | Etotal =23343.884 grad(E)=86.586 E(BOND)=2688.142 E(ANGL)=5440.285 | | E(DIHE)=0.000 E(IMPR)=5572.544 E(VDW )=729.430 E(CDIH)=1507.983 | | E(NOE )=7148.313 E(PLAN)=257.188 | ------------------------------------------------------------------------------- NBONDS: found 12419 intra-atom interactions NBONDS: found 12383 intra-atom interactions NBONDS: found 12416 intra-atom interactions NBONDS: found 12396 intra-atom interactions NBONDS: found 12426 intra-atom interactions NBONDS: found 12394 intra-atom interactions NBONDS: found 12396 intra-atom interactions NBONDS: found 12414 intra-atom interactions NBONDS: found 12429 intra-atom interactions NBONDS: found 12441 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=30041.448 E(kin)=6182.659 temperature=3063.767 | | Etotal =23858.790 grad(E)=91.770 E(BOND)=2897.935 E(ANGL)=5348.047 | | E(DIHE)=0.000 E(IMPR)=5586.108 E(VDW )=839.126 E(CDIH)=1581.794 | | E(NOE )=7279.623 E(PLAN)=326.156 | ------------------------------------------------------------------------------- NBONDS: found 12430 intra-atom interactions NBONDS: found 12375 intra-atom interactions NBONDS: found 12384 intra-atom interactions NBONDS: found 12376 intra-atom interactions NBONDS: found 12333 intra-atom interactions NBONDS: found 12296 intra-atom interactions NBONDS: found 12249 intra-atom interactions NBONDS: found 12184 intra-atom interactions NBONDS: found 12180 intra-atom interactions NBONDS: found 12153 intra-atom interactions NBONDS: found 12200 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=29373.879 E(kin)=6023.448 temperature=2984.871 | | Etotal =23350.431 grad(E)=93.216 E(BOND)=2456.417 E(ANGL)=5461.742 | | E(DIHE)=0.000 E(IMPR)=5543.545 E(VDW )=679.440 E(CDIH)=1470.607 | | E(NOE )=7476.971 E(PLAN)=261.709 | ------------------------------------------------------------------------------- NBONDS: found 12235 intra-atom interactions NBONDS: found 12297 intra-atom interactions NBONDS: found 12262 intra-atom interactions NBONDS: found 12252 intra-atom interactions NBONDS: found 12180 intra-atom interactions NBONDS: found 12129 intra-atom interactions NBONDS: found 12140 intra-atom interactions NBONDS: found 12104 intra-atom interactions NBONDS: found 12089 intra-atom interactions NBONDS: found 12063 intra-atom interactions NBONDS: found 12089 intra-atom interactions NBONDS: found 12068 intra-atom interactions NBONDS: found 12038 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=29378.739 E(kin)=6421.363 temperature=3182.055 | | Etotal =22957.376 grad(E)=90.849 E(BOND)=2771.748 E(ANGL)=5415.462 | | E(DIHE)=0.000 E(IMPR)=5301.505 E(VDW )=603.442 E(CDIH)=1206.704 | | E(NOE )=7484.048 E(PLAN)=174.467 | ------------------------------------------------------------------------------- NBONDS: found 12043 intra-atom interactions NBONDS: found 12068 intra-atom interactions NBONDS: found 12084 intra-atom interactions NBONDS: found 12104 intra-atom interactions NBONDS: found 12158 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00001 -0.00002 0.00000 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 -0.00002 0.00000 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 -0.00002 0.00000 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 12158 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=34288.012 E(kin)=6246.324 temperature=3095.316 | | Etotal =28041.688 grad(E)=100.495 E(BOND)=2871.516 E(ANGL)=5179.155 | | E(DIHE)=0.000 E(IMPR)=10851.441 E(VDW )=366.399 E(CDIH)=1131.142 | | E(NOE )=7416.499 E(PLAN)=225.535 | ------------------------------------------------------------------------------- NBONDS: found 12208 intra-atom interactions NBONDS: found 12200 intra-atom interactions NBONDS: found 12181 intra-atom interactions NBONDS: found 12182 intra-atom interactions NBONDS: found 12236 intra-atom interactions NBONDS: found 12250 intra-atom interactions NBONDS: found 12296 intra-atom interactions NBONDS: found 12391 intra-atom interactions NBONDS: found 12430 intra-atom interactions NBONDS: found 12500 intra-atom interactions NBONDS: found 12573 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=31914.706 E(kin)=6412.393 temperature=3177.610 | | Etotal =25502.313 grad(E)=99.218 E(BOND)=2819.757 E(ANGL)=6303.156 | | E(DIHE)=0.000 E(IMPR)=6471.006 E(VDW )=432.235 E(CDIH)=1333.638 | | E(NOE )=7925.062 E(PLAN)=217.460 | ------------------------------------------------------------------------------- NBONDS: found 12664 intra-atom interactions NBONDS: found 12670 intra-atom interactions NBONDS: found 12762 intra-atom interactions NBONDS: found 12821 intra-atom interactions NBONDS: found 12905 intra-atom interactions NBONDS: found 12918 intra-atom interactions NBONDS: found 12946 intra-atom interactions NBONDS: found 12940 intra-atom interactions NBONDS: found 12921 intra-atom interactions NBONDS: found 12920 intra-atom interactions NBONDS: found 12968 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=29893.413 E(kin)=6729.964 temperature=3334.980 | | Etotal =23163.450 grad(E)=88.697 E(BOND)=2917.627 E(ANGL)=6585.680 | | E(DIHE)=0.000 E(IMPR)=3569.683 E(VDW )=456.718 E(CDIH)=1537.455 | | E(NOE )=7885.862 E(PLAN)=210.425 | ------------------------------------------------------------------------------- NBONDS: found 13010 intra-atom interactions NBONDS: found 13079 intra-atom interactions NBONDS: found 13143 intra-atom interactions NBONDS: found 13205 intra-atom interactions NBONDS: found 13275 intra-atom interactions NBONDS: found 13352 intra-atom interactions NBONDS: found 13409 intra-atom interactions NBONDS: found 13470 intra-atom interactions NBONDS: found 13462 intra-atom interactions NBONDS: found 13491 intra-atom interactions NBONDS: found 13614 intra-atom interactions NBONDS: found 13688 intra-atom interactions NBONDS: found 13731 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=28390.409 E(kin)=6277.663 temperature=3110.846 | | Etotal =22112.746 grad(E)=100.990 E(BOND)=2895.143 E(ANGL)=5940.441 | | E(DIHE)=0.000 E(IMPR)=2750.549 E(VDW )=510.244 E(CDIH)=1457.131 | | E(NOE )=8334.009 E(PLAN)=225.227 | ------------------------------------------------------------------------------- NBONDS: found 13811 intra-atom interactions NBONDS: found 13872 intra-atom interactions NBONDS: found 13938 intra-atom interactions NBONDS: found 13961 intra-atom interactions NBONDS: found 13950 intra-atom interactions NBONDS: found 14022 intra-atom interactions NBONDS: found 14085 intra-atom interactions NBONDS: found 14199 intra-atom interactions NBONDS: found 14234 intra-atom interactions NBONDS: found 14231 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=27781.678 E(kin)=6796.865 temperature=3368.132 | | Etotal =20984.813 grad(E)=95.478 E(BOND)=2658.550 E(ANGL)=5685.758 | | E(DIHE)=0.000 E(IMPR)=1875.760 E(VDW )=530.092 E(CDIH)=1599.345 | | E(NOE )=8460.386 E(PLAN)=174.922 | ------------------------------------------------------------------------------- NBONDS: found 14245 intra-atom interactions NBONDS: found 14245 intra-atom interactions NBONDS: found 14246 intra-atom interactions NBONDS: found 14292 intra-atom interactions NBONDS: found 14293 intra-atom interactions NBONDS: found 14323 intra-atom interactions NBONDS: found 14325 intra-atom interactions NBONDS: found 14324 intra-atom interactions NBONDS: found 14368 intra-atom interactions NBONDS: found 14388 intra-atom interactions NBONDS: found 14406 intra-atom interactions NBONDS: found 14424 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=26891.004 E(kin)=6144.808 temperature=3045.010 | | Etotal =20746.197 grad(E)=96.182 E(BOND)=2553.176 E(ANGL)=6122.212 | | E(DIHE)=0.000 E(IMPR)=1680.504 E(VDW )=534.825 E(CDIH)=1441.319 | | E(NOE )=8192.093 E(PLAN)=222.067 | ------------------------------------------------------------------------------- NBONDS: found 14398 intra-atom interactions NBONDS: found 14424 intra-atom interactions NBONDS: found 14386 intra-atom interactions NBONDS: found 14381 intra-atom interactions NBONDS: found 14305 intra-atom interactions NBONDS: found 14277 intra-atom interactions NBONDS: found 14258 intra-atom interactions NBONDS: found 14243 intra-atom interactions NBONDS: found 14294 intra-atom interactions NBONDS: found 14341 intra-atom interactions NBONDS: found 14397 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=27308.625 E(kin)=6422.609 temperature=3182.672 | | Etotal =20886.016 grad(E)=94.927 E(BOND)=2543.070 E(ANGL)=5814.286 | | E(DIHE)=0.000 E(IMPR)=1991.363 E(VDW )=540.424 E(CDIH)=1487.393 | | E(NOE )=8305.831 E(PLAN)=203.651 | ------------------------------------------------------------------------------- NBONDS: found 14434 intra-atom interactions NBONDS: found 14528 intra-atom interactions NBONDS: found 14621 intra-atom interactions NBONDS: found 14686 intra-atom interactions NBONDS: found 14686 intra-atom interactions NBONDS: found 14773 intra-atom interactions NBONDS: found 14850 intra-atom interactions NBONDS: found 14915 intra-atom interactions NBONDS: found 14996 intra-atom interactions NBONDS: found 15056 intra-atom interactions NBONDS: found 15111 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=27053.223 E(kin)=6319.539 temperature=3131.597 | | Etotal =20733.684 grad(E)=95.959 E(BOND)=2852.635 E(ANGL)=5978.142 | | E(DIHE)=0.000 E(IMPR)=1720.362 E(VDW )=557.324 E(CDIH)=1620.212 | | E(NOE )=7867.546 E(PLAN)=137.463 | ------------------------------------------------------------------------------- NBONDS: found 15158 intra-atom interactions NBONDS: found 15243 intra-atom interactions NBONDS: found 15259 intra-atom interactions NBONDS: found 15302 intra-atom interactions NBONDS: found 15338 intra-atom interactions NBONDS: found 15394 intra-atom interactions NBONDS: found 15384 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00001 -0.00002 0.00000 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 -0.00002 0.00000 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 -0.00002 0.00000 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 14098 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=36930.354 E(kin)=6191.992 temperature=3068.392 | | Etotal =30738.362 grad(E)=194.879 E(BOND)=5355.955 E(ANGL)=11365.138 | | E(DIHE)=0.000 E(IMPR)=3870.617 E(VDW )=115.380 E(CDIH)=1545.010 | | E(NOE )=8283.780 E(PLAN)=202.481 | ------------------------------------------------------------------------------- NBONDS: found 14139 intra-atom interactions NBONDS: found 14177 intra-atom interactions NBONDS: found 14240 intra-atom interactions NBONDS: found 14282 intra-atom interactions NBONDS: found 14312 intra-atom interactions NBONDS: found 14324 intra-atom interactions NBONDS: found 14352 intra-atom interactions NBONDS: found 14365 intra-atom interactions NBONDS: found 14392 intra-atom interactions NBONDS: found 14430 intra-atom interactions NBONDS: found 14441 intra-atom interactions NBONDS: found 14435 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=31513.893 E(kin)=6850.409 temperature=3394.665 | | Etotal =24663.484 grad(E)=137.324 E(BOND)=2955.771 E(ANGL)=7032.126 | | E(DIHE)=0.000 E(IMPR)=2466.015 E(VDW )=122.847 E(CDIH)=2017.667 | | E(NOE )=9848.482 E(PLAN)=220.576 | ------------------------------------------------------------------------------- NBONDS: found 14450 intra-atom interactions NBONDS: found 14409 intra-atom interactions NBONDS: found 14358 intra-atom interactions NBONDS: found 14317 intra-atom interactions NBONDS: found 14285 intra-atom interactions NBONDS: found 14283 intra-atom interactions NBONDS: found 14342 intra-atom interactions NBONDS: found 14366 intra-atom interactions NBONDS: found 14334 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=30389.596 E(kin)=6257.687 temperature=3100.946 | | Etotal =24131.909 grad(E)=136.183 E(BOND)=2734.195 E(ANGL)=6856.031 | | E(DIHE)=0.000 E(IMPR)=2452.140 E(VDW )=116.594 E(CDIH)=1969.160 | | E(NOE )=9811.433 E(PLAN)=192.357 | ------------------------------------------------------------------------------- NBONDS: found 14329 intra-atom interactions NBONDS: found 14320 intra-atom interactions NBONDS: found 14297 intra-atom interactions NBONDS: found 14298 intra-atom interactions NBONDS: found 14334 intra-atom interactions NBONDS: found 14395 intra-atom interactions NBONDS: found 14413 intra-atom interactions NBONDS: found 14440 intra-atom interactions NBONDS: found 14495 intra-atom interactions NBONDS: found 14560 intra-atom interactions NBONDS: found 14649 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=29778.592 E(kin)=5872.437 temperature=2910.039 | | Etotal =23906.155 grad(E)=140.392 E(BOND)=2867.286 E(ANGL)=6941.659 | | E(DIHE)=0.000 E(IMPR)=1983.038 E(VDW )=120.983 E(CDIH)=1842.209 | | E(NOE )=9930.041 E(PLAN)=220.939 | ------------------------------------------------------------------------------- NBONDS: found 14705 intra-atom interactions NBONDS: found 14796 intra-atom interactions NBONDS: found 14873 intra-atom interactions NBONDS: found 14908 intra-atom interactions NBONDS: found 14953 intra-atom interactions NBONDS: found 14960 intra-atom interactions NBONDS: found 14978 intra-atom interactions NBONDS: found 14957 intra-atom interactions NBONDS: found 14924 intra-atom interactions NBONDS: found 14885 intra-atom interactions NBONDS: found 14866 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=29871.256 E(kin)=6368.451 temperature=3155.835 | | Etotal =23502.805 grad(E)=125.484 E(BOND)=2484.888 E(ANGL)=6494.031 | | E(DIHE)=0.000 E(IMPR)=2014.749 E(VDW )=128.079 E(CDIH)=1944.884 | | E(NOE )=10233.269 E(PLAN)=202.906 | ------------------------------------------------------------------------------- NBONDS: found 14829 intra-atom interactions NBONDS: found 14842 intra-atom interactions NBONDS: found 14832 intra-atom interactions NBONDS: found 14919 intra-atom interactions NBONDS: found 14971 intra-atom interactions NBONDS: found 15041 intra-atom interactions NBONDS: found 15038 intra-atom interactions NBONDS: found 15072 intra-atom interactions NBONDS: found 15114 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=29619.599 E(kin)=6282.428 temperature=3113.207 | | Etotal =23337.172 grad(E)=129.469 E(BOND)=2433.002 E(ANGL)=6779.320 | | E(DIHE)=0.000 E(IMPR)=1932.642 E(VDW )=127.848 E(CDIH)=1702.384 | | E(NOE )=10164.184 E(PLAN)=197.792 | ------------------------------------------------------------------------------- NBONDS: found 15183 intra-atom interactions NBONDS: found 15190 intra-atom interactions NBONDS: found 15216 intra-atom interactions NBONDS: found 15212 intra-atom interactions NBONDS: found 15194 intra-atom interactions NBONDS: found 15260 intra-atom interactions NBONDS: found 15363 intra-atom interactions NBONDS: found 15489 intra-atom interactions NBONDS: found 15602 intra-atom interactions NBONDS: found 15650 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=28902.541 E(kin)=6080.316 temperature=3013.052 | | Etotal =22822.224 grad(E)=133.738 E(BOND)=2380.044 E(ANGL)=6233.848 | | E(DIHE)=0.000 E(IMPR)=1728.376 E(VDW )=140.963 E(CDIH)=2019.229 | | E(NOE )=10121.482 E(PLAN)=198.282 | ------------------------------------------------------------------------------- NBONDS: found 15739 intra-atom interactions NBONDS: found 15768 intra-atom interactions NBONDS: found 15882 intra-atom interactions NBONDS: found 15960 intra-atom interactions NBONDS: found 16082 intra-atom interactions NBONDS: found 16138 intra-atom interactions NBONDS: found 16171 intra-atom interactions NBONDS: found 16219 intra-atom interactions NBONDS: found 16239 intra-atom interactions NBONDS: found 16301 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=28411.115 E(kin)=6624.351 temperature=3282.644 | | Etotal =21786.764 grad(E)=119.980 E(BOND)=2435.206 E(ANGL)=6683.763 | | E(DIHE)=0.000 E(IMPR)=1531.534 E(VDW )=148.208 E(CDIH)=1731.669 | | E(NOE )=9115.984 E(PLAN)=140.400 | ------------------------------------------------------------------------------- NBONDS: found 16433 intra-atom interactions NBONDS: found 16518 intra-atom interactions NBONDS: found 16575 intra-atom interactions NBONDS: found 16717 intra-atom interactions NBONDS: found 16873 intra-atom interactions NBONDS: found 16982 intra-atom interactions NBONDS: found 17108 intra-atom interactions NBONDS: found 17190 intra-atom interactions NBONDS: found 17234 intra-atom interactions NBONDS: found 17248 intra-atom interactions --------------- step= 800 at 1.60000 ps -------------------------------- | E(kin)+E(total)=28498.471 E(kin)=6409.073 temperature=3175.965 | | Etotal =22089.398 grad(E)=140.730 E(BOND)=2668.119 E(ANGL)=6579.926 | | E(DIHE)=0.000 E(IMPR)=1618.514 E(VDW )=164.205 E(CDIH)=1651.524 | | E(NOE )=9268.795 E(PLAN)=138.315 | ------------------------------------------------------------------------------- NBONDS: found 17238 intra-atom interactions NBONDS: found 17214 intra-atom interactions NBONDS: found 17208 intra-atom interactions NBONDS: found 17174 intra-atom interactions NBONDS: found 17180 intra-atom interactions NBONDS: found 17122 intra-atom interactions NBONDS: found 17044 intra-atom interactions NBONDS: found 16979 intra-atom interactions NBONDS: found 16904 intra-atom interactions NBONDS: found 16853 intra-atom interactions NBONDS: found 16841 intra-atom interactions NBONDS: found 16856 intra-atom interactions --------------- step= 900 at 1.80000 ps -------------------------------- | E(kin)+E(total)=27326.274 E(kin)=6146.791 temperature=3045.993 | | Etotal =21179.483 grad(E)=124.427 E(BOND)=2401.017 E(ANGL)=6610.861 | | E(DIHE)=0.000 E(IMPR)=1587.771 E(VDW )=152.815 E(CDIH)=1505.881 | | E(NOE )=8766.272 E(PLAN)=154.867 | ------------------------------------------------------------------------------- NBONDS: found 16892 intra-atom interactions NBONDS: found 16851 intra-atom interactions NBONDS: found 16832 intra-atom interactions NBONDS: found 16861 intra-atom interactions NBONDS: found 16902 intra-atom interactions NBONDS: found 16863 intra-atom interactions NBONDS: found 16755 intra-atom interactions NBONDS: found 16691 intra-atom interactions NBONDS: found 16649 intra-atom interactions NBONDS: found 16642 intra-atom interactions --------------- step= 1000 at 2.00000 ps -------------------------------- | E(kin)+E(total)=27568.935 E(kin)=6182.855 temperature=3063.864 | | Etotal =21386.079 grad(E)=129.954 E(BOND)=2548.205 E(ANGL)=6696.104 | | E(DIHE)=0.000 E(IMPR)=1456.725 E(VDW )=147.283 E(CDIH)=1591.357 | | E(NOE )=8759.171 E(PLAN)=187.234 | ------------------------------------------------------------------------------- NBONDS: found 16637 intra-atom interactions NBONDS: found 16687 intra-atom interactions NBONDS: found 16675 intra-atom interactions NBONDS: found 16645 intra-atom interactions NBONDS: found 16621 intra-atom interactions NBONDS: found 16648 intra-atom interactions NBONDS: found 16688 intra-atom interactions NBONDS: found 16747 intra-atom interactions NBONDS: found 16873 intra-atom interactions --------------- step= 1100 at 2.20000 ps -------------------------------- | E(kin)+E(total)=27296.562 E(kin)=5984.012 temperature=2965.329 | | Etotal =21312.550 grad(E)=126.337 E(BOND)=2496.505 E(ANGL)=6136.931 | | E(DIHE)=0.000 E(IMPR)=1567.442 E(VDW )=157.299 E(CDIH)=1558.168 | | E(NOE )=9208.486 E(PLAN)=187.720 | ------------------------------------------------------------------------------- NBONDS: found 17037 intra-atom interactions NBONDS: found 17210 intra-atom interactions NBONDS: found 17390 intra-atom interactions NBONDS: found 17583 intra-atom interactions NBONDS: found 17744 intra-atom interactions NBONDS: found 17885 intra-atom interactions NBONDS: found 17995 intra-atom interactions NBONDS: found 18139 intra-atom interactions NBONDS: found 18260 intra-atom interactions NBONDS: found 18355 intra-atom interactions --------------- step= 1200 at 2.40000 ps -------------------------------- | E(kin)+E(total)=27400.848 E(kin)=5875.823 temperature=2911.717 | | Etotal =21525.025 grad(E)=126.674 E(BOND)=2626.253 E(ANGL)=6549.529 | | E(DIHE)=0.000 E(IMPR)=1487.011 E(VDW )=181.592 E(CDIH)=1559.225 | | E(NOE )=8943.698 E(PLAN)=177.719 | ------------------------------------------------------------------------------- NBONDS: found 18363 intra-atom interactions NBONDS: found 18365 intra-atom interactions NBONDS: found 18371 intra-atom interactions NBONDS: found 18388 intra-atom interactions NBONDS: found 18401 intra-atom interactions NBONDS: found 18376 intra-atom interactions NBONDS: found 18398 intra-atom interactions NBONDS: found 18468 intra-atom interactions NBONDS: found 18503 intra-atom interactions NBONDS: found 18523 intra-atom interactions --------------- step= 1300 at 2.60000 ps -------------------------------- | E(kin)+E(total)=27606.878 E(kin)=6003.532 temperature=2975.002 | | Etotal =21603.346 grad(E)=132.599 E(BOND)=2645.589 E(ANGL)=6362.987 | | E(DIHE)=0.000 E(IMPR)=1559.814 E(VDW )=192.897 E(CDIH)=1578.485 | | E(NOE )=9130.050 E(PLAN)=133.524 | ------------------------------------------------------------------------------- NBONDS: found 18534 intra-atom interactions NBONDS: found 18514 intra-atom interactions NBONDS: found 18452 intra-atom interactions NBONDS: found 18475 intra-atom interactions NBONDS: found 18493 intra-atom interactions NBONDS: found 18565 intra-atom interactions NBONDS: found 18668 intra-atom interactions NBONDS: found 18696 intra-atom interactions NBONDS: found 18733 intra-atom interactions NBONDS: found 18674 intra-atom interactions --------------- step= 1400 at 2.80000 ps -------------------------------- | E(kin)+E(total)=27262.554 E(kin)=5782.386 temperature=2865.415 | | Etotal =21480.167 grad(E)=129.518 E(BOND)=2617.808 E(ANGL)=6482.567 | | E(DIHE)=0.000 E(IMPR)=1429.968 E(VDW )=204.351 E(CDIH)=1503.940 | | E(NOE )=9134.841 E(PLAN)=106.692 | ------------------------------------------------------------------------------- NBONDS: found 18663 intra-atom interactions NBONDS: found 18634 intra-atom interactions NBONDS: found 18681 intra-atom interactions NBONDS: found 18711 intra-atom interactions NBONDS: found 18685 intra-atom interactions NBONDS: found 18647 intra-atom interactions NBONDS: found 18538 intra-atom interactions NBONDS: found 18523 intra-atom interactions NBONDS: found 18582 intra-atom interactions NBONDS: found 18508 intra-atom interactions --------------- step= 1500 at 3.00000 ps -------------------------------- | E(kin)+E(total)=27730.505 E(kin)=6038.490 temperature=2992.325 | | Etotal =21692.016 grad(E)=130.964 E(BOND)=2510.914 E(ANGL)=6808.104 | | E(DIHE)=0.000 E(IMPR)=1332.099 E(VDW )=202.839 E(CDIH)=1619.036 | | E(NOE )=9084.401 E(PLAN)=134.623 | ------------------------------------------------------------------------------- NBONDS: found 18402 intra-atom interactions NBONDS: found 18311 intra-atom interactions NBONDS: found 18217 intra-atom interactions NBONDS: found 18262 intra-atom interactions NBONDS: found 18222 intra-atom interactions NBONDS: found 18227 intra-atom interactions NBONDS: found 18257 intra-atom interactions NBONDS: found 18274 intra-atom interactions NBONDS: found 18259 intra-atom interactions --------------- step= 1600 at 3.20000 ps -------------------------------- | E(kin)+E(total)=27863.385 E(kin)=6302.481 temperature=3123.144 | | Etotal =21560.904 grad(E)=132.575 E(BOND)=2786.821 E(ANGL)=6490.369 | | E(DIHE)=0.000 E(IMPR)=1344.869 E(VDW )=196.259 E(CDIH)=1602.518 | | E(NOE )=8999.954 E(PLAN)=140.114 | ------------------------------------------------------------------------------- NBONDS: found 18246 intra-atom interactions NBONDS: found 18275 intra-atom interactions NBONDS: found 18313 intra-atom interactions NBONDS: found 18243 intra-atom interactions NBONDS: found 18238 intra-atom interactions NBONDS: found 18251 intra-atom interactions NBONDS: found 18237 intra-atom interactions NBONDS: found 18234 intra-atom interactions NBONDS: found 18253 intra-atom interactions --------------- step= 1700 at 3.40000 ps -------------------------------- | E(kin)+E(total)=27771.461 E(kin)=6247.326 temperature=3095.812 | | Etotal =21524.135 grad(E)=132.573 E(BOND)=2616.528 E(ANGL)=5868.868 | | E(DIHE)=0.000 E(IMPR)=1436.437 E(VDW )=193.263 E(CDIH)=1554.719 | | E(NOE )=9733.422 E(PLAN)=120.898 | ------------------------------------------------------------------------------- NBONDS: found 18244 intra-atom interactions NBONDS: found 18215 intra-atom interactions NBONDS: found 18143 intra-atom interactions NBONDS: found 18087 intra-atom interactions NBONDS: found 18081 intra-atom interactions NBONDS: found 18067 intra-atom interactions NBONDS: found 17952 intra-atom interactions NBONDS: found 17920 intra-atom interactions NBONDS: found 17845 intra-atom interactions NBONDS: found 17759 intra-atom interactions --------------- step= 1800 at 3.60000 ps -------------------------------- | E(kin)+E(total)=26998.124 E(kin)=6589.095 temperature=3265.173 | | Etotal =20409.030 grad(E)=126.573 E(BOND)=2346.644 E(ANGL)=5837.066 | | E(DIHE)=0.000 E(IMPR)=1261.750 E(VDW )=174.256 E(CDIH)=1460.161 | | E(NOE )=9176.308 E(PLAN)=152.845 | ------------------------------------------------------------------------------- NBONDS: found 17675 intra-atom interactions NBONDS: found 17650 intra-atom interactions NBONDS: found 17628 intra-atom interactions NBONDS: found 17605 intra-atom interactions NBONDS: found 17554 intra-atom interactions NBONDS: found 17491 intra-atom interactions NBONDS: found 17481 intra-atom interactions NBONDS: found 17427 intra-atom interactions NBONDS: found 17355 intra-atom interactions NBONDS: found 17248 intra-atom interactions NBONDS: found 17128 intra-atom interactions NBONDS: found 17053 intra-atom interactions --------------- step= 1900 at 3.80000 ps -------------------------------- | E(kin)+E(total)=26344.382 E(kin)=6104.362 temperature=3024.968 | | Etotal =20240.019 grad(E)=122.122 E(BOND)=2411.924 E(ANGL)=5862.286 | | E(DIHE)=0.000 E(IMPR)=1271.769 E(VDW )=162.640 E(CDIH)=1492.099 | | E(NOE )=8833.529 E(PLAN)=205.772 | ------------------------------------------------------------------------------- NBONDS: found 17049 intra-atom interactions NBONDS: found 17018 intra-atom interactions NBONDS: found 17038 intra-atom interactions NBONDS: found 17046 intra-atom interactions NBONDS: found 17034 intra-atom interactions NBONDS: found 17141 intra-atom interactions NBONDS: found 17227 intra-atom interactions NBONDS: found 17282 intra-atom interactions NBONDS: found 17332 intra-atom interactions --------------- step= 2000 at 4.00000 ps -------------------------------- | E(kin)+E(total)=26294.016 E(kin)=5808.911 temperature=2878.559 | | Etotal =20485.105 grad(E)=130.447 E(BOND)=2622.975 E(ANGL)=5681.412 | | E(DIHE)=0.000 E(IMPR)=1324.765 E(VDW )=163.663 E(CDIH)=1634.709 | | E(NOE )=8829.558 E(PLAN)=228.023 | ------------------------------------------------------------------------------- NBONDS: found 17444 intra-atom interactions NBONDS: found 17428 intra-atom interactions NBONDS: found 17525 intra-atom interactions NBONDS: found 17600 intra-atom interactions NBONDS: found 17616 intra-atom interactions NBONDS: found 17632 intra-atom interactions NBONDS: found 17653 intra-atom interactions NBONDS: found 17748 intra-atom interactions NBONDS: found 17793 intra-atom interactions NBONDS: found 17833 intra-atom interactions --------------- step= 2100 at 4.20000 ps -------------------------------- | E(kin)+E(total)=26441.063 E(kin)=5986.561 temperature=2966.592 | | Etotal =20454.502 grad(E)=125.187 E(BOND)=2554.884 E(ANGL)=5727.922 | | E(DIHE)=0.000 E(IMPR)=1342.664 E(VDW )=174.533 E(CDIH)=1664.764 | | E(NOE )=8749.528 E(PLAN)=240.207 | ------------------------------------------------------------------------------- NBONDS: found 17840 intra-atom interactions NBONDS: found 17903 intra-atom interactions NBONDS: found 17876 intra-atom interactions NBONDS: found 17811 intra-atom interactions NBONDS: found 17808 intra-atom interactions NBONDS: found 17748 intra-atom interactions NBONDS: found 17620 intra-atom interactions NBONDS: found 17540 intra-atom interactions --------------- step= 2200 at 4.40000 ps -------------------------------- | E(kin)+E(total)=26113.427 E(kin)=5926.270 temperature=2936.715 | | Etotal =20187.157 grad(E)=129.302 E(BOND)=2590.143 E(ANGL)=6115.246 | | E(DIHE)=0.000 E(IMPR)=1567.331 E(VDW )=171.390 E(CDIH)=1523.029 | | E(NOE )=8002.714 E(PLAN)=217.303 | ------------------------------------------------------------------------------- NBONDS: found 17504 intra-atom interactions NBONDS: found 17501 intra-atom interactions NBONDS: found 17517 intra-atom interactions NBONDS: found 17541 intra-atom interactions NBONDS: found 17533 intra-atom interactions NBONDS: found 17578 intra-atom interactions NBONDS: found 17632 intra-atom interactions NBONDS: found 17715 intra-atom interactions NBONDS: found 17746 intra-atom interactions --------------- step= 2300 at 4.60000 ps -------------------------------- | E(kin)+E(total)=26163.329 E(kin)=6124.949 temperature=3035.170 | | Etotal =20038.380 grad(E)=133.226 E(BOND)=2583.718 E(ANGL)=5974.503 | | E(DIHE)=0.000 E(IMPR)=1183.181 E(VDW )=173.488 E(CDIH)=1514.046 | | E(NOE )=8421.984 E(PLAN)=187.460 | ------------------------------------------------------------------------------- NBONDS: found 17773 intra-atom interactions NBONDS: found 17790 intra-atom interactions NBONDS: found 17768 intra-atom interactions NBONDS: found 17816 intra-atom interactions NBONDS: found 17941 intra-atom interactions NBONDS: found 17966 intra-atom interactions NBONDS: found 18006 intra-atom interactions NBONDS: found 18010 intra-atom interactions NBONDS: found 18017 intra-atom interactions --------------- step= 2400 at 4.80000 ps -------------------------------- | E(kin)+E(total)=26223.465 E(kin)=6087.058 temperature=3016.393 | | Etotal =20136.407 grad(E)=126.271 E(BOND)=2386.947 E(ANGL)=5709.392 | | E(DIHE)=0.000 E(IMPR)=1456.173 E(VDW )=183.358 E(CDIH)=1391.980 | | E(NOE )=8791.785 E(PLAN)=216.772 | ------------------------------------------------------------------------------- NBONDS: found 18046 intra-atom interactions NBONDS: found 18071 intra-atom interactions NBONDS: found 18161 intra-atom interactions NBONDS: found 18266 intra-atom interactions NBONDS: found 18367 intra-atom interactions NBONDS: found 18432 intra-atom interactions NBONDS: found 18490 intra-atom interactions NBONDS: found 18469 intra-atom interactions NBONDS: found 18592 intra-atom interactions --------------- step= 2500 at 5.00000 ps -------------------------------- | E(kin)+E(total)=25902.840 E(kin)=5948.002 temperature=2947.485 | | Etotal =19954.837 grad(E)=129.372 E(BOND)=2652.181 E(ANGL)=5864.937 | | E(DIHE)=0.000 E(IMPR)=1409.910 E(VDW )=202.601 E(CDIH)=1469.601 | | E(NOE )=8165.037 E(PLAN)=190.570 | ------------------------------------------------------------------------------- NBONDS: found 18574 intra-atom interactions NBONDS: found 18534 intra-atom interactions NBONDS: found 18575 intra-atom interactions NBONDS: found 18593 intra-atom interactions NBONDS: found 18587 intra-atom interactions NBONDS: found 18594 intra-atom interactions NBONDS: found 18647 intra-atom interactions NBONDS: found 18594 intra-atom interactions --------------- step= 2600 at 5.20000 ps -------------------------------- | E(kin)+E(total)=26185.410 E(kin)=6011.886 temperature=2979.142 | | Etotal =20173.524 grad(E)=129.903 E(BOND)=2620.995 E(ANGL)=6262.138 | | E(DIHE)=0.000 E(IMPR)=1255.445 E(VDW )=205.008 E(CDIH)=1391.188 | | E(NOE )=8262.937 E(PLAN)=175.814 | ------------------------------------------------------------------------------- NBONDS: found 18665 intra-atom interactions NBONDS: found 18682 intra-atom interactions NBONDS: found 18710 intra-atom interactions NBONDS: found 18817 intra-atom interactions NBONDS: found 18947 intra-atom interactions NBONDS: found 18993 intra-atom interactions NBONDS: found 19065 intra-atom interactions NBONDS: found 19118 intra-atom interactions NBONDS: found 19099 intra-atom interactions --------------- step= 2700 at 5.40000 ps -------------------------------- | E(kin)+E(total)=26163.350 E(kin)=6144.047 temperature=3044.633 | | Etotal =20019.302 grad(E)=131.670 E(BOND)=2564.469 E(ANGL)=5880.352 | | E(DIHE)=0.000 E(IMPR)=1325.619 E(VDW )=216.199 E(CDIH)=1411.447 | | E(NOE )=8449.464 E(PLAN)=171.753 | ------------------------------------------------------------------------------- NBONDS: found 19067 intra-atom interactions NBONDS: found 19071 intra-atom interactions NBONDS: found 19041 intra-atom interactions NBONDS: found 19093 intra-atom interactions NBONDS: found 19085 intra-atom interactions NBONDS: found 18954 intra-atom interactions NBONDS: found 18907 intra-atom interactions NBONDS: found 18886 intra-atom interactions NBONDS: found 18838 intra-atom interactions --------------- step= 2800 at 5.60000 ps -------------------------------- | E(kin)+E(total)=25987.559 E(kin)=6062.539 temperature=3004.242 | | Etotal =19925.020 grad(E)=129.457 E(BOND)=2532.333 E(ANGL)=5561.726 | | E(DIHE)=0.000 E(IMPR)=1362.401 E(VDW )=210.618 E(CDIH)=1562.563 | | E(NOE )=8439.801 E(PLAN)=255.578 | ------------------------------------------------------------------------------- NBONDS: found 18851 intra-atom interactions NBONDS: found 18784 intra-atom interactions NBONDS: found 18810 intra-atom interactions NBONDS: found 18829 intra-atom interactions NBONDS: found 18792 intra-atom interactions NBONDS: found 18865 intra-atom interactions NBONDS: found 18930 intra-atom interactions NBONDS: found 18966 intra-atom interactions --------------- step= 2900 at 5.80000 ps -------------------------------- | E(kin)+E(total)=26079.424 E(kin)=5903.309 temperature=2925.337 | | Etotal =20176.116 grad(E)=132.544 E(BOND)=2384.830 E(ANGL)=5895.405 | | E(DIHE)=0.000 E(IMPR)=1473.733 E(VDW )=209.847 E(CDIH)=1502.336 | | E(NOE )=8521.907 E(PLAN)=188.057 | ------------------------------------------------------------------------------- NBONDS: found 18981 intra-atom interactions NBONDS: found 18961 intra-atom interactions NBONDS: found 18992 intra-atom interactions NBONDS: found 19094 intra-atom interactions NBONDS: found 19083 intra-atom interactions NBONDS: found 19012 intra-atom interactions NBONDS: found 19033 intra-atom interactions NBONDS: found 18934 intra-atom interactions --------------- step= 3000 at 6.00000 ps -------------------------------- | E(kin)+E(total)=26044.429 E(kin)=6186.508 temperature=3065.674 | | Etotal =19857.921 grad(E)=125.579 E(BOND)=2635.989 E(ANGL)=5499.273 | | E(DIHE)=0.000 E(IMPR)=1274.717 E(VDW )=212.999 E(CDIH)=1400.865 | | E(NOE )=8620.215 E(PLAN)=213.861 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 0.00001 -0.00002 0.00000 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 -0.00002 0.00000 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 -0.00002 0.00000 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 18855 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=40159.398 E(kin)=6186.508 temperature=3065.674 | | Etotal =33972.890 grad(E)=312.508 E(BOND)=6589.973 E(ANGL)=13748.184 | | E(DIHE)=0.000 E(IMPR)=3186.792 E(VDW )=212.999 E(CDIH)=1400.865 | | E(NOE )=8620.215 E(PLAN)=213.861 | ------------------------------------------------------------------------------- NBONDS: found 18810 intra-atom interactions NBONDS: found 18823 intra-atom interactions NBONDS: found 18896 intra-atom interactions NBONDS: found 18971 intra-atom interactions NBONDS: found 19012 intra-atom interactions NBONDS: found 18974 intra-atom interactions NBONDS: found 18890 intra-atom interactions NBONDS: found 18853 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=32983.436 E(kin)=6711.985 temperature=3326.070 | | Etotal =26271.451 grad(E)=218.683 E(BOND)=2628.163 E(ANGL)=8596.837 | | E(DIHE)=0.000 E(IMPR)=1794.143 E(VDW )=209.705 E(CDIH)=1716.164 | | E(NOE )=10978.075 E(PLAN)=348.362 | ------------------------------------------------------------------------------- NBONDS: found 18927 intra-atom interactions NBONDS: found 19076 intra-atom interactions NBONDS: found 19121 intra-atom interactions NBONDS: found 19140 intra-atom interactions NBONDS: found 19070 intra-atom interactions NBONDS: found 19154 intra-atom interactions NBONDS: found 19208 intra-atom interactions NBONDS: found 19210 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=31762.478 E(kin)=6457.857 temperature=3200.139 | | Etotal =25304.621 grad(E)=205.210 E(BOND)=2864.779 E(ANGL)=7092.972 | | E(DIHE)=0.000 E(IMPR)=1679.450 E(VDW )=219.242 E(CDIH)=1483.130 | | E(NOE )=11601.188 E(PLAN)=363.859 | ------------------------------------------------------------------------------- NBONDS: found 19186 intra-atom interactions NBONDS: found 19216 intra-atom interactions NBONDS: found 19239 intra-atom interactions NBONDS: found 19300 intra-atom interactions NBONDS: found 19352 intra-atom interactions NBONDS: found 19359 intra-atom interactions NBONDS: found 19378 intra-atom interactions NBONDS: found 19342 intra-atom interactions NBONDS: found 19302 intra-atom interactions NBONDS: found 19270 intra-atom interactions NBONDS: found 19216 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=30735.739 E(kin)=6405.460 temperature=3174.174 | | Etotal =24330.279 grad(E)=190.394 E(BOND)=2360.456 E(ANGL)=7238.012 | | E(DIHE)=0.000 E(IMPR)=1397.334 E(VDW )=228.245 E(CDIH)=1107.193 | | E(NOE )=11614.499 E(PLAN)=384.540 | ------------------------------------------------------------------------------- NBONDS: found 19182 intra-atom interactions NBONDS: found 19149 intra-atom interactions NBONDS: found 19194 intra-atom interactions NBONDS: found 19204 intra-atom interactions NBONDS: found 19206 intra-atom interactions NBONDS: found 19180 intra-atom interactions NBONDS: found 19202 intra-atom interactions NBONDS: found 19234 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=30367.738 E(kin)=6054.976 temperature=3000.495 | | Etotal =24312.762 grad(E)=196.813 E(BOND)=2663.753 E(ANGL)=7618.699 | | E(DIHE)=0.000 E(IMPR)=1226.909 E(VDW )=227.341 E(CDIH)=1215.571 | | E(NOE )=11011.549 E(PLAN)=348.941 | ------------------------------------------------------------------------------- NBONDS: found 19227 intra-atom interactions NBONDS: found 19195 intra-atom interactions NBONDS: found 19316 intra-atom interactions NBONDS: found 19341 intra-atom interactions NBONDS: found 19372 intra-atom interactions NBONDS: found 19474 intra-atom interactions NBONDS: found 19539 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=30506.506 E(kin)=6181.979 temperature=3063.430 | | Etotal =24324.527 grad(E)=192.687 E(BOND)=2427.352 E(ANGL)=7741.139 | | E(DIHE)=0.000 E(IMPR)=1381.033 E(VDW )=238.627 E(CDIH)=1216.790 | | E(NOE )=10944.920 E(PLAN)=374.666 | ------------------------------------------------------------------------------- NBONDS: found 19532 intra-atom interactions NBONDS: found 19494 intra-atom interactions NBONDS: found 19583 intra-atom interactions NBONDS: found 19610 intra-atom interactions NBONDS: found 19642 intra-atom interactions NBONDS: found 19710 intra-atom interactions NBONDS: found 19761 intra-atom interactions NBONDS: found 19804 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=30477.439 E(kin)=6172.026 temperature=3058.498 | | Etotal =24305.413 grad(E)=190.418 E(BOND)=2419.682 E(ANGL)=7458.612 | | E(DIHE)=0.000 E(IMPR)=1456.730 E(VDW )=241.477 E(CDIH)=1385.314 | | E(NOE )=10939.031 E(PLAN)=404.566 | ------------------------------------------------------------------------------- NBONDS: found 19754 intra-atom interactions NBONDS: found 19721 intra-atom interactions NBONDS: found 19581 intra-atom interactions NBONDS: found 19527 intra-atom interactions NBONDS: found 19490 intra-atom interactions NBONDS: found 19496 intra-atom interactions NBONDS: found 19530 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=30359.596 E(kin)=6199.019 temperature=3071.874 | | Etotal =24160.577 grad(E)=193.673 E(BOND)=2425.542 E(ANGL)=7679.171 | | E(DIHE)=0.000 E(IMPR)=1414.665 E(VDW )=229.140 E(CDIH)=1297.645 | | E(NOE )=10698.232 E(PLAN)=416.181 | ------------------------------------------------------------------------------- NBONDS: found 19551 intra-atom interactions NBONDS: found 19530 intra-atom interactions NBONDS: found 19614 intra-atom interactions NBONDS: found 19690 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00001 -0.00002 0.00000 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 17:24:34 created by user: COOR>ATOM 1 P GUA 1 12.388 6.391 7.044 1.00 0.00 A COOR>ATOM 2 O1P GUA 1 14.128 6.272 5.783 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 = 2.4642 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.7472 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.7227 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0608 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8705 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8354 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1269 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.2162 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.8090 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.4573 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.8324 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.0531 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.8174 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.9042 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.5025 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1813 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.7080 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9604 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2597 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8974 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.7155 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 15271 intra-atom interactions NBONDS: found 15338 intra-atom interactions NBONDS: found 15424 intra-atom interactions NBONDS: found 15531 intra-atom interactions NBONDS: found 15646 intra-atom interactions NBONDS: found 15649 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0002 ----------------------- | Etotal =107900.419 grad(E)=301.963 E(BOND)=14313.547 E(VDW )=11484.119 | | E(CDIH)=4285.014 E(NOE )=77220.699 E(PLAN)=597.040 | ------------------------------------------------------------------------------- NBONDS: found 15713 intra-atom interactions NBONDS: found 15713 intra-atom interactions NBONDS: found 15653 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0002 ----------------------- | Etotal =59814.315 grad(E)=224.041 E(BOND)=5768.491 E(VDW )=8419.876 | | E(CDIH)=3061.881 E(NOE )=42263.318 E(PLAN)=300.748 | ------------------------------------------------------------------------------- NBONDS: found 15588 intra-atom interactions NBONDS: found 15525 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0002 ----------------------- | Etotal =40746.219 grad(E)=125.265 E(BOND)=2355.432 E(VDW )=6170.464 | | E(CDIH)=2561.628 E(NOE )=29455.614 E(PLAN)=203.082 | ------------------------------------------------------------------------------- NBONDS: found 15454 intra-atom interactions NBONDS: found 15394 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0002 ----------------------- | Etotal =32185.095 grad(E)=88.119 E(BOND)=1448.668 E(VDW )=4520.056 | | E(CDIH)=2199.917 E(NOE )=23798.057 E(PLAN)=218.397 | ------------------------------------------------------------------------------- NBONDS: found 15288 intra-atom interactions NBONDS: found 15175 intra-atom interactions NBONDS: found 15054 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0002 ----------------------- | Etotal =25325.998 grad(E)=85.159 E(BOND)=1164.907 E(VDW )=3258.588 | | E(CDIH)=1529.127 E(NOE )=19084.736 E(PLAN)=288.640 | ------------------------------------------------------------------------------- NBONDS: found 14984 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =21197.615 grad(E)=56.981 E(BOND)=886.602 E(VDW )=2734.099 | | E(CDIH)=1222.935 E(NOE )=16026.946 E(PLAN)=327.032 | ------------------------------------------------------------------------------- NBONDS: found 14846 intra-atom interactions NBONDS: found 14358 intra-atom interactions NBONDS: found 14811 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0002 ----------------------- | Etotal =18632.751 grad(E)=54.296 E(BOND)=667.683 E(VDW )=2122.137 | | E(CDIH)=1466.470 E(NOE )=14049.446 E(PLAN)=327.015 | ------------------------------------------------------------------------------- NBONDS: found 14697 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0002 ----------------------- | Etotal =16267.822 grad(E)=42.472 E(BOND)=520.495 E(VDW )=1581.558 | | E(CDIH)=1104.391 E(NOE )=12763.284 E(PLAN)=298.093 | ------------------------------------------------------------------------------- NBONDS: found 14595 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0002 ----------------------- | Etotal =14819.160 grad(E)=48.044 E(BOND)=426.706 E(VDW )=1242.316 | | E(CDIH)=1078.250 E(NOE )=11798.887 E(PLAN)=273.001 | ------------------------------------------------------------------------------- NBONDS: found 14510 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =14103.843 grad(E)=28.544 E(BOND)=300.095 E(VDW )=1219.737 | | E(CDIH)=837.973 E(NOE )=11476.489 E(PLAN)=269.548 | ------------------------------------------------------------------------------- --------------- cycle= 110 ------ stepsize= 0.0000 ----------------------- | Etotal =14079.978 grad(E)=26.518 E(BOND)=289.108 E(VDW )=1216.973 | | E(CDIH)=835.052 E(NOE )=11469.271 E(PLAN)=269.574 | ------------------------------------------------------------------------------- --------------- cycle= 120 ------ stepsize= 0.0000 ----------------------- | Etotal =14183.344 grad(E)=32.764 E(BOND)=289.030 E(VDW )=1216.952 | | E(CDIH)=938.572 E(NOE )=11469.216 E(PLAN)=269.574 | ------------------------------------------------------------------------------- --------------- cycle= 130 ------ stepsize= 0.0000 ----------------------- | Etotal =14079.808 grad(E)=26.504 E(BOND)=289.032 E(VDW )=1216.953 | | E(CDIH)=835.031 E(NOE )=11469.218 E(PLAN)=269.574 | ------------------------------------------------------------------------------- --------------- cycle= 140 ------ stepsize= 0.0000 ----------------------- | Etotal =14079.808 grad(E)=26.504 E(BOND)=289.032 E(VDW )=1216.953 | | E(CDIH)=835.031 E(NOE )=11469.218 E(PLAN)=269.574 | ------------------------------------------------------------------------------- %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 14428 intra-atom interactions NBONDS: found 14406 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =99052.001 grad(E)=325.742 E(BOND)=11193.107 E(ANGL)=66510.141 | | E(VDW )=2669.162 E(CDIH)=2280.209 E(NOE )=15835.822 E(PLAN)=563.560 | ------------------------------------------------------------------------------- NBONDS: found 14385 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =69002.082 grad(E)=183.197 E(BOND)=4368.860 E(ANGL)=36775.069 | | E(VDW )=3634.984 E(CDIH)=2748.016 E(NOE )=20795.097 E(PLAN)=680.057 | ------------------------------------------------------------------------------- NBONDS: found 14333 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =56542.714 grad(E)=101.626 E(BOND)=2968.994 E(ANGL)=26008.138 | | E(VDW )=3813.836 E(CDIH)=3034.098 E(NOE )=20069.294 E(PLAN)=648.354 | ------------------------------------------------------------------------------- NBONDS: found 14358 intra-atom interactions NBONDS: found 14287 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =50797.406 grad(E)=92.103 E(BOND)=2550.890 E(ANGL)=21953.150 | | E(VDW )=3702.237 E(CDIH)=3062.574 E(NOE )=18910.528 E(PLAN)=618.026 | ------------------------------------------------------------------------------- NBONDS: found 14177 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =47388.581 grad(E)=86.273 E(BOND)=2199.183 E(ANGL)=19356.689 | | E(VDW )=3671.884 E(CDIH)=2973.084 E(NOE )=18601.894 E(PLAN)=585.847 | ------------------------------------------------------------------------------- NBONDS: found 14087 intra-atom interactions NBONDS: found 14031 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =43963.897 grad(E)=76.478 E(BOND)=2163.789 E(ANGL)=15940.834 | | E(VDW )=3528.280 E(CDIH)=2907.447 E(NOE )=18852.361 E(PLAN)=571.185 | ------------------------------------------------------------------------------- NBONDS: found 13968 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =41088.442 grad(E)=64.115 E(BOND)=1760.408 E(ANGL)=14099.005 | | E(VDW )=3457.607 E(CDIH)=2936.954 E(NOE )=18289.959 E(PLAN)=544.510 | ------------------------------------------------------------------------------- NBONDS: found 13931 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =39339.845 grad(E)=56.913 E(BOND)=1589.335 E(ANGL)=13123.598 | | E(VDW )=3460.037 E(CDIH)=2821.539 E(NOE )=17824.887 E(PLAN)=520.448 | ------------------------------------------------------------------------------- NBONDS: found 13843 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =37755.308 grad(E)=60.612 E(BOND)=1481.963 E(ANGL)=12340.358 | | E(VDW )=3294.416 E(CDIH)=2864.861 E(NOE )=17276.130 E(PLAN)=497.579 | ------------------------------------------------------------------------------- NBONDS: found 13786 intra-atom interactions NBONDS: found 13746 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =36290.622 grad(E)=51.846 E(BOND)=1388.424 E(ANGL)=11828.211 | | E(VDW )=3152.692 E(CDIH)=2843.197 E(NOE )=16605.283 E(PLAN)=472.816 | ------------------------------------------------------------------------------- NBONDS: found 13678 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0001 ----------------------- | Etotal =35219.967 grad(E)=41.925 E(BOND)=1297.328 E(ANGL)=11687.964 | | E(VDW )=3069.948 E(CDIH)=2824.617 E(NOE )=15891.540 E(PLAN)=448.569 | ------------------------------------------------------------------------------- NBONDS: found 13619 intra-atom interactions NBONDS: found 13591 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0001 ----------------------- | Etotal =34103.827 grad(E)=36.967 E(BOND)=1293.482 E(ANGL)=11310.685 | | E(VDW )=2962.906 E(CDIH)=2815.739 E(NOE )=15285.601 E(PLAN)=435.414 | ------------------------------------------------------------------------------- NBONDS: found 13546 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0001 ----------------------- | Etotal =33441.281 grad(E)=27.514 E(BOND)=1211.535 E(ANGL)=11201.409 | | E(VDW )=2918.244 E(CDIH)=2783.076 E(NOE )=14918.085 E(PLAN)=408.933 | ------------------------------------------------------------------------------- NBONDS: found 13446 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0001 ----------------------- | Etotal =32574.667 grad(E)=39.199 E(BOND)=1210.529 E(ANGL)=10694.496 | | E(VDW )=2794.028 E(CDIH)=2724.103 E(NOE )=14776.369 E(PLAN)=375.142 | ------------------------------------------------------------------------------- NBONDS: found 13388 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =31813.433 grad(E)=41.115 E(BOND)=1110.677 E(ANGL)=10542.153 | | E(VDW )=2640.947 E(CDIH)=2662.963 E(NOE )=14499.068 E(PLAN)=357.626 | ------------------------------------------------------------------------------- NBONDS: found 13295 intra-atom interactions --------------- cycle= 160 ------ stepsize= 0.0001 ----------------------- | Etotal =31073.062 grad(E)=31.723 E(BOND)=1063.085 E(ANGL)=10288.224 | | E(VDW )=2526.788 E(CDIH)=2605.071 E(NOE )=14244.033 E(PLAN)=345.861 | ------------------------------------------------------------------------------- NBONDS: found 13224 intra-atom interactions --------------- cycle= 170 ------ stepsize= 0.0001 ----------------------- | Etotal =30490.377 grad(E)=32.133 E(BOND)=1013.589 E(ANGL)=10115.430 | | E(VDW )=2371.612 E(CDIH)=2559.998 E(NOE )=14104.706 E(PLAN)=325.042 | ------------------------------------------------------------------------------- NBONDS: found 13083 intra-atom interactions --------------- cycle= 180 ------ stepsize= 0.0001 ----------------------- | Etotal =29987.822 grad(E)=26.308 E(BOND)=963.347 E(ANGL)=9952.945 | | E(VDW )=2243.850 E(CDIH)=2525.158 E(NOE )=14011.711 E(PLAN)=290.812 | ------------------------------------------------------------------------------- NBONDS: found 12961 intra-atom interactions --------------- cycle= 190 ------ stepsize= 0.0001 ----------------------- | Etotal =29344.748 grad(E)=32.974 E(BOND)=1039.292 E(ANGL)=9582.663 | | E(VDW )=2013.318 E(CDIH)=2499.988 E(NOE )=13942.686 E(PLAN)=266.801 | ------------------------------------------------------------------------------- NBONDS: found 12801 intra-atom interactions NBONDS: found 12697 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =28601.437 grad(E)=35.317 E(BOND)=1007.790 E(ANGL)=9157.425 | | E(VDW )=1686.792 E(CDIH)=2501.939 E(NOE )=13989.176 E(PLAN)=258.314 | ------------------------------------------------------------------------------- NBONDS: found 12574 intra-atom interactions --------------- cycle= 210 ------ stepsize= 0.0001 ----------------------- | Etotal =27825.320 grad(E)=34.810 E(BOND)=1031.009 E(ANGL)=8676.329 | | E(VDW )=1452.785 E(CDIH)=2518.745 E(NOE )=13888.743 E(PLAN)=257.709 | ------------------------------------------------------------------------------- NBONDS: found 12489 intra-atom interactions --------------- cycle= 220 ------ stepsize= 0.0001 ----------------------- | Etotal =27154.196 grad(E)=29.972 E(BOND)=979.597 E(ANGL)=8321.927 | | E(VDW )=1412.612 E(CDIH)=2495.344 E(NOE )=13691.849 E(PLAN)=252.867 | ------------------------------------------------------------------------------- NBONDS: found 12412 intra-atom interactions --------------- cycle= 230 ------ stepsize= 0.0001 ----------------------- | Etotal =26580.626 grad(E)=32.007 E(BOND)=923.681 E(ANGL)=8071.770 | | E(VDW )=1405.448 E(CDIH)=2475.557 E(NOE )=13461.288 E(PLAN)=242.882 | ------------------------------------------------------------------------------- NBONDS: found 12270 intra-atom interactions --------------- cycle= 240 ------ stepsize= 0.0001 ----------------------- | Etotal =26069.646 grad(E)=29.079 E(BOND)=871.768 E(ANGL)=8016.071 | | E(VDW )=1255.333 E(CDIH)=2476.774 E(NOE )=13220.994 E(PLAN)=228.706 | ------------------------------------------------------------------------------- NBONDS: found 12105 intra-atom interactions --------------- cycle= 250 ------ stepsize= 0.0001 ----------------------- | Etotal =25729.566 grad(E)=25.480 E(BOND)=866.279 E(ANGL)=7927.225 | | E(VDW )=1132.122 E(CDIH)=2433.246 E(NOE )=13144.992 E(PLAN)=225.702 | ------------------------------------------------------------------------------- --------------- cycle= 260 ------ stepsize= 0.0001 ----------------------- | Etotal =25409.011 grad(E)=25.051 E(BOND)=803.991 E(ANGL)=7810.190 | | E(VDW )=1071.063 E(CDIH)=2385.624 E(NOE )=13101.934 E(PLAN)=236.208 | ------------------------------------------------------------------------------- --------------- cycle= 270 ------ stepsize= 0.0001 ----------------------- | Etotal =25074.013 grad(E)=23.956 E(BOND)=768.876 E(ANGL)=7667.827 | | E(VDW )=1058.602 E(CDIH)=2355.403 E(NOE )=12976.919 E(PLAN)=246.387 | ------------------------------------------------------------------------------- NBONDS: found 12003 intra-atom interactions --------------- cycle= 280 ------ stepsize= 0.0001 ----------------------- | Etotal =24811.287 grad(E)=22.420 E(BOND)=764.607 E(ANGL)=7657.194 | | E(VDW )=1004.533 E(CDIH)=2309.714 E(NOE )=12817.928 E(PLAN)=257.311 | ------------------------------------------------------------------------------- NBONDS: found 12010 intra-atom interactions --------------- cycle= 290 ------ stepsize= 0.0001 ----------------------- | Etotal =24575.250 grad(E)=21.666 E(BOND)=758.248 E(ANGL)=7657.467 | | E(VDW )=943.883 E(CDIH)=2264.677 E(NOE )=12690.965 E(PLAN)=260.009 | ------------------------------------------------------------------------------- --------------- cycle= 300 ------ stepsize= 0.0001 ----------------------- | Etotal =24347.003 grad(E)=18.931 E(BOND)=750.065 E(ANGL)=7647.369 | | E(VDW )=925.651 E(CDIH)=2212.468 E(NOE )=12549.435 E(PLAN)=262.015 | ------------------------------------------------------------------------------- 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= 505177093. ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : -0.00001 -0.00002 0.00000 velocity [A/ps] : -0.19228 -0.00285 0.14328 ang. mom. [amu A/ps] : 120018.71696-222640.84154 108605.85522 kin. ener. [Kcal/mol] : 4.65268 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : -0.00001 -0.00002 0.00000 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 11986 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=29626.524 E(kin)=5855.362 temperature=2901.578 | | Etotal =23771.162 grad(E)=69.149 E(BOND)=75.006 E(ANGL)=764.737 | | E(DIHE)=0.000 E(IMPR)=6981.849 E(VDW )=925.651 E(CDIH)=2212.468 | | E(NOE )=12549.435 E(PLAN)=262.015 | ------------------------------------------------------------------------------- NBONDS: found 11976 intra-atom interactions NBONDS: found 12000 intra-atom interactions NBONDS: found 12004 intra-atom interactions NBONDS: found 11965 intra-atom interactions NBONDS: found 11974 intra-atom interactions NBONDS: found 11973 intra-atom interactions NBONDS: found 11932 intra-atom interactions NBONDS: found 11936 intra-atom interactions NBONDS: found 11879 intra-atom interactions NBONDS: found 11817 intra-atom interactions NBONDS: found 11732 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=27955.233 E(kin)=7164.886 temperature=3550.502 | | Etotal =20790.347 grad(E)=66.270 E(BOND)=2780.717 E(ANGL)=4084.185 | | E(DIHE)=0.000 E(IMPR)=3565.299 E(VDW )=373.943 E(CDIH)=1468.891 | | E(NOE )=8282.650 E(PLAN)=234.661 | ------------------------------------------------------------------------------- NBONDS: found 11699 intra-atom interactions NBONDS: found 11662 intra-atom interactions NBONDS: found 11641 intra-atom interactions NBONDS: found 11577 intra-atom interactions NBONDS: found 11548 intra-atom interactions NBONDS: found 11447 intra-atom interactions NBONDS: found 11353 intra-atom interactions NBONDS: found 11315 intra-atom interactions NBONDS: found 11276 intra-atom interactions NBONDS: found 11231 intra-atom interactions NBONDS: found 11196 intra-atom interactions NBONDS: found 11160 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=24645.564 E(kin)=7055.593 temperature=3496.342 | | Etotal =17589.971 grad(E)=64.164 E(BOND)=2236.136 E(ANGL)=4107.156 | | E(DIHE)=0.000 E(IMPR)=2917.654 E(VDW )=247.737 E(CDIH)=1151.208 | | E(NOE )=6690.167 E(PLAN)=239.913 | ------------------------------------------------------------------------------- NBONDS: found 11142 intra-atom interactions NBONDS: found 11118 intra-atom interactions NBONDS: found 11113 intra-atom interactions NBONDS: found 11087 intra-atom interactions NBONDS: found 11075 intra-atom interactions NBONDS: found 11085 intra-atom interactions NBONDS: found 11069 intra-atom interactions NBONDS: found 11033 intra-atom interactions NBONDS: found 11023 intra-atom interactions NBONDS: found 10987 intra-atom interactions NBONDS: found 10963 intra-atom interactions NBONDS: found 10925 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=20878.626 E(kin)=6609.600 temperature=3275.334 | | Etotal =14269.026 grad(E)=62.423 E(BOND)=2315.671 E(ANGL)=3114.967 | | E(DIHE)=0.000 E(IMPR)=2524.738 E(VDW )=496.528 E(CDIH)=777.744 | | E(NOE )=4834.353 E(PLAN)=205.025 | ------------------------------------------------------------------------------- NBONDS: found 10887 intra-atom interactions NBONDS: found 10889 intra-atom interactions NBONDS: found 10862 intra-atom interactions NBONDS: found 10850 intra-atom interactions NBONDS: found 10802 intra-atom interactions NBONDS: found 10763 intra-atom interactions NBONDS: found 10692 intra-atom interactions NBONDS: found 10661 intra-atom interactions NBONDS: found 10614 intra-atom interactions NBONDS: found 10603 intra-atom interactions NBONDS: found 10505 intra-atom interactions NBONDS: found 10454 intra-atom interactions NBONDS: found 10403 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=18697.316 E(kin)=6487.128 temperature=3214.644 | | Etotal =12210.188 grad(E)=57.725 E(BOND)=1932.637 E(ANGL)=3225.534 | | E(DIHE)=0.000 E(IMPR)=2394.487 E(VDW )=171.661 E(CDIH)=587.722 | | E(NOE )=3730.165 E(PLAN)=167.982 | ------------------------------------------------------------------------------- NBONDS: found 10419 intra-atom interactions NBONDS: found 10382 intra-atom interactions NBONDS: found 10392 intra-atom interactions NBONDS: found 10393 intra-atom interactions NBONDS: found 10417 intra-atom interactions NBONDS: found 10412 intra-atom interactions NBONDS: found 10431 intra-atom interactions NBONDS: found 10445 intra-atom interactions NBONDS: found 10426 intra-atom interactions NBONDS: found 10409 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=17913.835 E(kin)=6038.278 temperature=2992.220 | | Etotal =11875.557 grad(E)=59.736 E(BOND)=1836.503 E(ANGL)=3343.066 | | E(DIHE)=0.000 E(IMPR)=2003.678 E(VDW )=101.864 E(CDIH)=509.048 | | E(NOE )=3944.227 E(PLAN)=137.172 | ------------------------------------------------------------------------------- NBONDS: found 10409 intra-atom interactions NBONDS: found 10451 intra-atom interactions NBONDS: found 10433 intra-atom interactions NBONDS: found 10423 intra-atom interactions NBONDS: found 10420 intra-atom interactions NBONDS: found 10404 intra-atom interactions NBONDS: found 10362 intra-atom interactions NBONDS: found 10367 intra-atom interactions NBONDS: found 10362 intra-atom interactions NBONDS: found 10352 intra-atom interactions NBONDS: found 10334 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=17282.227 E(kin)=6464.167 temperature=3203.266 | | Etotal =10818.060 grad(E)=58.749 E(BOND)=1739.238 E(ANGL)=3387.152 | | E(DIHE)=0.000 E(IMPR)=1707.652 E(VDW )=146.115 E(CDIH)=465.743 | | E(NOE )=3267.634 E(PLAN)=104.527 | ------------------------------------------------------------------------------- NBONDS: found 10338 intra-atom interactions NBONDS: found 10337 intra-atom interactions NBONDS: found 10308 intra-atom interactions NBONDS: found 10316 intra-atom interactions NBONDS: found 10320 intra-atom interactions NBONDS: found 10323 intra-atom interactions NBONDS: found 10313 intra-atom interactions NBONDS: found 10306 intra-atom interactions NBONDS: found 10305 intra-atom interactions NBONDS: found 10313 intra-atom interactions NBONDS: found 10315 intra-atom interactions NBONDS: found 10284 intra-atom interactions NBONDS: found 10312 intra-atom interactions NBONDS: found 10320 intra-atom interactions NBONDS: found 10322 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=16028.596 E(kin)=6139.289 temperature=3042.275 | | Etotal =9889.307 grad(E)=60.663 E(BOND)=1870.643 E(ANGL)=3105.469 | | E(DIHE)=0.000 E(IMPR)=1361.422 E(VDW )=143.242 E(CDIH)=447.232 | | E(NOE )=2803.091 E(PLAN)=158.209 | ------------------------------------------------------------------------------- NBONDS: found 10333 intra-atom interactions NBONDS: found 10342 intra-atom interactions NBONDS: found 10339 intra-atom interactions NBONDS: found 10319 intra-atom interactions NBONDS: found 10296 intra-atom interactions NBONDS: found 10293 intra-atom interactions CENMAS: Information about center of free masses position [A] : -0.00001 -0.00002 0.00000 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 -0.00002 0.00000 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 -0.00002 0.00000 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 10296 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=22009.520 E(kin)=6177.592 temperature=3061.256 | | Etotal =15831.929 grad(E)=111.834 E(BOND)=3802.707 E(ANGL)=6475.996 | | E(DIHE)=0.000 E(IMPR)=2245.572 E(VDW )=136.822 E(CDIH)=406.343 | | E(NOE )=2628.524 E(PLAN)=135.965 | ------------------------------------------------------------------------------- NBONDS: found 10279 intra-atom interactions NBONDS: found 10225 intra-atom interactions NBONDS: found 10241 intra-atom interactions NBONDS: found 10245 intra-atom interactions NBONDS: found 10304 intra-atom interactions NBONDS: found 10316 intra-atom interactions NBONDS: found 10320 intra-atom interactions NBONDS: found 10309 intra-atom interactions NBONDS: found 10293 intra-atom interactions NBONDS: found 10261 intra-atom interactions NBONDS: found 10220 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=17403.909 E(kin)=6791.286 temperature=3365.368 | | Etotal =10612.623 grad(E)=81.379 E(BOND)=1910.681 E(ANGL)=3513.168 | | E(DIHE)=0.000 E(IMPR)=1634.211 E(VDW )=149.359 E(CDIH)=454.658 | | E(NOE )=2784.954 E(PLAN)=165.593 | ------------------------------------------------------------------------------- NBONDS: found 10187 intra-atom interactions NBONDS: found 10164 intra-atom interactions NBONDS: found 10178 intra-atom interactions NBONDS: found 10209 intra-atom interactions NBONDS: found 10180 intra-atom interactions NBONDS: found 10131 intra-atom interactions NBONDS: found 10082 intra-atom interactions NBONDS: found 10065 intra-atom interactions NBONDS: found 10033 intra-atom interactions NBONDS: found 10073 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=16675.901 E(kin)=6290.172 temperature=3117.044 | | Etotal =10385.728 grad(E)=79.977 E(BOND)=1906.589 E(ANGL)=3274.153 | | E(DIHE)=0.000 E(IMPR)=1698.661 E(VDW )=207.506 E(CDIH)=464.571 | | E(NOE )=2630.781 E(PLAN)=203.468 | ------------------------------------------------------------------------------- NBONDS: found 10073 intra-atom interactions NBONDS: found 10067 intra-atom interactions NBONDS: found 10091 intra-atom interactions NBONDS: found 10063 intra-atom interactions NBONDS: found 10044 intra-atom interactions NBONDS: found 9977 intra-atom interactions NBONDS: found 9940 intra-atom interactions NBONDS: found 9903 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=16667.753 E(kin)=6465.158 temperature=3203.757 | | Etotal =10202.595 grad(E)=81.787 E(BOND)=1880.060 E(ANGL)=3356.615 | | E(DIHE)=0.000 E(IMPR)=1505.901 E(VDW )=215.481 E(CDIH)=468.620 | | E(NOE )=2637.608 E(PLAN)=138.310 | ------------------------------------------------------------------------------- NBONDS: found 9887 intra-atom interactions NBONDS: found 9862 intra-atom interactions NBONDS: found 9863 intra-atom interactions NBONDS: found 9862 intra-atom interactions NBONDS: found 9806 intra-atom interactions NBONDS: found 9763 intra-atom interactions NBONDS: found 9764 intra-atom interactions NBONDS: found 9807 intra-atom interactions NBONDS: found 9823 intra-atom interactions NBONDS: found 9858 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=16372.608 E(kin)=6189.738 temperature=3067.275 | | Etotal =10182.870 grad(E)=85.225 E(BOND)=1880.256 E(ANGL)=3208.654 | | E(DIHE)=0.000 E(IMPR)=1767.557 E(VDW )=150.699 E(CDIH)=536.989 | | E(NOE )=2512.561 E(PLAN)=126.154 | ------------------------------------------------------------------------------- NBONDS: found 9864 intra-atom interactions NBONDS: found 9865 intra-atom interactions NBONDS: found 9878 intra-atom interactions NBONDS: found 9874 intra-atom interactions NBONDS: found 9888 intra-atom interactions NBONDS: found 9919 intra-atom interactions NBONDS: found 9936 intra-atom interactions NBONDS: found 9941 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=16405.739 E(kin)=6074.821 temperature=3010.329 | | Etotal =10330.918 grad(E)=85.672 E(BOND)=1936.749 E(ANGL)=3104.907 | | E(DIHE)=0.000 E(IMPR)=1671.883 E(VDW )=185.236 E(CDIH)=42