X-PLOR: V3.840 user: on: Alpha/OSF at: 16-Aug-96 17:06:33 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=55678.4261169434 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 17:03:07 created by user: COOR>ATOM 1 P GUA 1 13.541 2.340 -8.461 1.00 0.00 A COOR>ATOM 2 O1P GUA 1 11.861 4.493 -9.451 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 = 2.9014 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.8269 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9607 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9028 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2765 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9157 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0091 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.2908 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6720 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.3796 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.7209 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.3645 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.0475 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.3262 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.3914 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0391 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.6485 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9529 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.4532 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9685 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6519 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 15477 intra-atom interactions NBONDS: found 15549 intra-atom interactions NBONDS: found 15631 intra-atom interactions NBONDS: found 15675 intra-atom interactions NBONDS: found 15751 intra-atom interactions NBONDS: found 15793 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0002 ----------------------- | Etotal =108276.543 grad(E)=322.222 E(BOND)=14158.226 E(VDW )=12575.358 | | E(CDIH)=4552.509 E(NOE )=76410.933 E(PLAN)=579.517 | ------------------------------------------------------------------------------- NBONDS: found 15821 intra-atom interactions NBONDS: found 15824 intra-atom interactions NBONDS: found 15832 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =59698.852 grad(E)=198.337 E(BOND)=5020.448 E(VDW )=9909.203 | | E(CDIH)=3129.369 E(NOE )=41257.405 E(PLAN)=382.426 | ------------------------------------------------------------------------------- NBONDS: found 15778 intra-atom interactions NBONDS: found 15755 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =39997.388 grad(E)=108.269 E(BOND)=2114.209 E(VDW )=7073.095 | | E(CDIH)=2794.254 E(NOE )=27809.557 E(PLAN)=206.273 | ------------------------------------------------------------------------------- NBONDS: found 15709 intra-atom interactions NBONDS: found 15557 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0002 ----------------------- | Etotal =30423.247 grad(E)=101.681 E(BOND)=1490.873 E(VDW )=5081.298 | | E(CDIH)=2398.543 E(NOE )=21194.504 E(PLAN)=258.029 | ------------------------------------------------------------------------------- NBONDS: found 15494 intra-atom interactions NBONDS: found 15401 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0002 ----------------------- | Etotal =24626.686 grad(E)=67.098 E(BOND)=952.038 E(VDW )=3553.918 | | E(CDIH)=1988.733 E(NOE )=17816.282 E(PLAN)=315.714 | ------------------------------------------------------------------------------- NBONDS: found 15338 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0002 ----------------------- | Etotal =21211.876 grad(E)=68.216 E(BOND)=791.132 E(VDW )=2848.564 | | E(CDIH)=1802.089 E(NOE )=15464.574 E(PLAN)=305.518 | ------------------------------------------------------------------------------- NBONDS: found 15224 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0002 ----------------------- | Etotal =18944.193 grad(E)=44.882 E(BOND)=542.868 E(VDW )=2487.237 | | E(CDIH)=1857.001 E(NOE )=13784.298 E(PLAN)=272.789 | ------------------------------------------------------------------------------- NBONDS: found 14912 intra-atom interactions NBONDS: found 15171 intra-atom interactions NBONDS: found 14971 intra-atom interactions NBONDS: found 15090 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =17098.583 grad(E)=40.585 E(BOND)=444.845 E(VDW )=2253.035 | | E(CDIH)=1505.991 E(NOE )=12623.291 E(PLAN)=271.421 | ------------------------------------------------------------------------------- --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =15851.386 grad(E)=35.020 E(BOND)=428.563 E(VDW )=1949.269 | | E(CDIH)=1406.870 E(NOE )=11795.562 E(PLAN)=271.121 | ------------------------------------------------------------------------------- NBONDS: found 14968 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =15106.523 grad(E)=33.370 E(BOND)=371.088 E(VDW )=1895.503 | | E(CDIH)=1305.680 E(NOE )=11269.005 E(PLAN)=265.247 | ------------------------------------------------------------------------------- NBONDS: found 14780 intra-atom interactions NBONDS: found 14934 intra-atom interactions NBONDS: found 14743 intra-atom interactions NBONDS: found 14869 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0000 ----------------------- | Etotal =14539.469 grad(E)=45.321 E(BOND)=396.342 E(VDW )=1840.275 | | E(CDIH)=1425.751 E(NOE )=10627.220 E(PLAN)=249.881 | ------------------------------------------------------------------------------- --------------- cycle= 120 ------ stepsize= 0.0000 ----------------------- | Etotal =14369.176 grad(E)=35.763 E(BOND)=390.819 E(VDW )=1844.753 | | E(CDIH)=1347.277 E(NOE )=10537.838 E(PLAN)=248.489 | ------------------------------------------------------------------------------- --------------- cycle= 130 ------ stepsize= 0.0000 ----------------------- | Etotal =14501.297 grad(E)=44.703 E(BOND)=391.373 E(VDW )=1844.912 | | E(CDIH)=1481.134 E(NOE )=10535.424 E(PLAN)=248.455 | ------------------------------------------------------------------------------- --------------- cycle= 140 ------ stepsize= 0.0000 ----------------------- | Etotal =14365.862 grad(E)=35.634 E(BOND)=391.362 E(VDW )=1844.908 | | E(CDIH)=1345.664 E(NOE )=10535.473 E(PLAN)=248.455 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =14365.859 grad(E)=35.633 E(BOND)=391.362 E(VDW )=1844.909 | | E(CDIH)=1345.662 E(NOE )=10535.471 E(PLAN)=248.455 | ------------------------------------------------------------------------------- --------------- cycle= 160 ------ stepsize= 0.0000 ----------------------- | Etotal =14365.859 grad(E)=35.633 E(BOND)=391.362 E(VDW )=1844.909 | | E(CDIH)=1345.662 E(NOE )=10535.471 E(PLAN)=248.455 | ------------------------------------------------------------------------------- %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 14799 intra-atom interactions NBONDS: found 14772 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =97365.653 grad(E)=350.689 E(BOND)=11645.650 E(ANGL)=63564.727 | | E(VDW )=3947.222 E(CDIH)=2918.821 E(NOE )=14855.553 E(PLAN)=433.679 | ------------------------------------------------------------------------------- NBONDS: found 14768 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =65792.884 grad(E)=166.353 E(BOND)=4515.147 E(ANGL)=33710.274 | | E(VDW )=4612.156 E(CDIH)=3405.184 E(NOE )=19040.381 E(PLAN)=509.742 | ------------------------------------------------------------------------------- NBONDS: found 14748 intra-atom interactions NBONDS: found 14742 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =57034.979 grad(E)=94.859 E(BOND)=2609.374 E(ANGL)=25157.207 | | E(VDW )=4963.370 E(CDIH)=3582.065 E(NOE )=20197.085 E(PLAN)=525.876 | ------------------------------------------------------------------------------- NBONDS: found 14671 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =50963.585 grad(E)=100.604 E(BOND)=2592.939 E(ANGL)=21726.789 | | E(VDW )=4599.318 E(CDIH)=3701.092 E(NOE )=17823.511 E(PLAN)=519.937 | ------------------------------------------------------------------------------- NBONDS: found 14547 intra-atom interactions NBONDS: found 14430 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =45989.076 grad(E)=89.781 E(BOND)=2138.718 E(ANGL)=17031.810 | | E(VDW )=4289.315 E(CDIH)=3937.186 E(NOE )=18077.731 E(PLAN)=514.316 | ------------------------------------------------------------------------------- NBONDS: found 14363 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =42333.207 grad(E)=75.097 E(BOND)=2042.869 E(ANGL)=14694.486 | | E(VDW )=4057.264 E(CDIH)=3872.192 E(NOE )=17159.804 E(PLAN)=506.591 | ------------------------------------------------------------------------------- NBONDS: found 14293 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =39998.224 grad(E)=45.765 E(BOND)=1832.218 E(ANGL)=14110.301 | | E(VDW )=3749.986 E(CDIH)=3771.657 E(NOE )=16035.970 E(PLAN)=498.093 | ------------------------------------------------------------------------------- NBONDS: found 14193 intra-atom interactions NBONDS: found 14137 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =38716.363 grad(E)=44.224 E(BOND)=1655.715 E(ANGL)=13451.575 | | E(VDW )=3635.414 E(CDIH)=3758.657 E(NOE )=15732.830 E(PLAN)=482.172 | ------------------------------------------------------------------------------- --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =37526.416 grad(E)=48.104 E(BOND)=1488.417 E(ANGL)=13281.855 | | E(VDW )=3535.394 E(CDIH)=3732.472 E(NOE )=15015.099 E(PLAN)=473.179 | ------------------------------------------------------------------------------- NBONDS: found 14036 intra-atom interactions NBONDS: found 13959 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =36260.662 grad(E)=42.709 E(BOND)=1426.200 E(ANGL)=12657.847 | | E(VDW )=3362.782 E(CDIH)=3675.744 E(NOE )=14645.637 E(PLAN)=492.452 | ------------------------------------------------------------------------------- NBONDS: found 13897 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0001 ----------------------- | Etotal =35387.595 grad(E)=33.928 E(BOND)=1367.921 E(ANGL)=12289.393 | | E(VDW )=3274.609 E(CDIH)=3633.143 E(NOE )=14313.490 E(PLAN)=509.037 | ------------------------------------------------------------------------------- NBONDS: found 13828 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0001 ----------------------- | Etotal =34437.120 grad(E)=45.453 E(BOND)=1344.432 E(ANGL)=12169.708 | | E(VDW )=3104.667 E(CDIH)=3560.881 E(NOE )=13721.360 E(PLAN)=536.073 | ------------------------------------------------------------------------------- NBONDS: found 13779 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0001 ----------------------- | Etotal =33619.569 grad(E)=39.117 E(BOND)=1244.495 E(ANGL)=11886.412 | | E(VDW )=3023.654 E(CDIH)=3522.903 E(NOE )=13382.496 E(PLAN)=559.609 | ------------------------------------------------------------------------------- NBONDS: found 13719 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0001 ----------------------- | Etotal =32876.248 grad(E)=42.109 E(BOND)=1185.644 E(ANGL)=11644.598 | | E(VDW )=2949.020 E(CDIH)=3491.760 E(NOE )=13056.555 E(PLAN)=548.671 | ------------------------------------------------------------------------------- NBONDS: found 13705 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =32246.298 grad(E)=27.619 E(BOND)=1085.278 E(ANGL)=11553.428 | | E(VDW )=2890.306 E(CDIH)=3465.237 E(NOE )=12715.830 E(PLAN)=536.219 | ------------------------------------------------------------------------------- NBONDS: found 13626 intra-atom interactions --------------- cycle= 160 ------ stepsize= 0.0001 ----------------------- | Etotal =31801.883 grad(E)=26.384 E(BOND)=1049.377 E(ANGL)=11505.587 | | E(VDW )=2839.459 E(CDIH)=3436.589 E(NOE )=12442.661 E(PLAN)=528.210 | ------------------------------------------------------------------------------- --------------- cycle= 170 ------ stepsize= 0.0001 ----------------------- | Etotal =31386.156 grad(E)=23.333 E(BOND)=1015.429 E(ANGL)=11500.844 | | E(VDW )=2813.669 E(CDIH)=3377.760 E(NOE )=12163.736 E(PLAN)=514.718 | ------------------------------------------------------------------------------- NBONDS: found 13576 intra-atom interactions --------------- cycle= 180 ------ stepsize= 0.0001 ----------------------- | Etotal =31037.314 grad(E)=20.872 E(BOND)=957.276 E(ANGL)=11472.617 | | E(VDW )=2741.668 E(CDIH)=3333.730 E(NOE )=12040.196 E(PLAN)=491.827 | ------------------------------------------------------------------------------- NBONDS: found 13493 intra-atom interactions --------------- cycle= 190 ------ stepsize= 0.0001 ----------------------- | Etotal =30540.996 grad(E)=28.014 E(BOND)=988.295 E(ANGL)=11366.578 | | E(VDW )=2494.800 E(CDIH)=3227.610 E(NOE )=12016.941 E(PLAN)=446.772 | ------------------------------------------------------------------------------- NBONDS: found 13429 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =30068.244 grad(E)=25.618 E(BOND)=1017.517 E(ANGL)=11293.239 | | E(VDW )=2260.908 E(CDIH)=3175.384 E(NOE )=11903.222 E(PLAN)=417.974 | ------------------------------------------------------------------------------- NBONDS: found 13340 intra-atom interactions --------------- cycle= 210 ------ stepsize= 0.0001 ----------------------- | Etotal =29621.979 grad(E)=25.928 E(BOND)=1000.637 E(ANGL)=11042.129 | | E(VDW )=2080.772 E(CDIH)=3168.598 E(NOE )=11929.643 E(PLAN)=400.200 | ------------------------------------------------------------------------------- NBONDS: found 13243 intra-atom interactions --------------- cycle= 220 ------ stepsize= 0.0001 ----------------------- | Etotal =29119.496 grad(E)=37.812 E(BOND)=918.434 E(ANGL)=10694.502 | | E(VDW )=1990.236 E(CDIH)=3159.563 E(NOE )=11975.932 E(PLAN)=380.828 | ------------------------------------------------------------------------------- NBONDS: found 13157 intra-atom interactions NBONDS: found 13079 intra-atom interactions --------------- cycle= 230 ------ stepsize= 0.0001 ----------------------- | Etotal =28489.772 grad(E)=30.198 E(BOND)=880.958 E(ANGL)=10542.547 | | E(VDW )=1962.254 E(CDIH)=3171.451 E(NOE )=11559.202 E(PLAN)=373.360 | ------------------------------------------------------------------------------- NBONDS: found 13026 intra-atom interactions NBONDS: found 12943 intra-atom interactions --------------- cycle= 240 ------ stepsize= 0.0001 ----------------------- | Etotal =27862.327 grad(E)=30.517 E(BOND)=878.091 E(ANGL)=10648.180 | | E(VDW )=1839.050 E(CDIH)=3136.598 E(NOE )=10983.763 E(PLAN)=376.646 | ------------------------------------------------------------------------------- --------------- cycle= 250 ------ stepsize= 0.0001 ----------------------- | Etotal =27417.340 grad(E)=24.725 E(BOND)=823.471 E(ANGL)=10534.217 | | E(VDW )=1820.374 E(CDIH)=3098.096 E(NOE )=10769.537 E(PLAN)=371.645 | ------------------------------------------------------------------------------- NBONDS: found 12870 intra-atom interactions --------------- cycle= 260 ------ stepsize= 0.0001 ----------------------- | Etotal =27080.620 grad(E)=21.807 E(BOND)=814.104 E(ANGL)=10318.556 | | E(VDW )=1862.052 E(CDIH)=3089.867 E(NOE )=10637.534 E(PLAN)=358.507 | ------------------------------------------------------------------------------- NBONDS: found 12773 intra-atom interactions --------------- cycle= 270 ------ stepsize= 0.0001 ----------------------- | Etotal =26748.758 grad(E)=22.092 E(BOND)=770.705 E(ANGL)=10214.207 | | E(VDW )=1874.391 E(CDIH)=3074.165 E(NOE )=10471.580 E(PLAN)=343.709 | ------------------------------------------------------------------------------- --------------- cycle= 280 ------ stepsize= 0.0001 ----------------------- | Etotal =26440.727 grad(E)=21.921 E(BOND)=754.683 E(ANGL)=10250.501 | | E(VDW )=1852.077 E(CDIH)=3045.963 E(NOE )=10205.046 E(PLAN)=332.458 | ------------------------------------------------------------------------------- NBONDS: found 12583 intra-atom interactions --------------- cycle= 290 ------ stepsize= 0.0001 ----------------------- | Etotal =26213.364 grad(E)=17.211 E(BOND)=743.553 E(ANGL)=10115.891 | | E(VDW )=1839.138 E(CDIH)=3057.071 E(NOE )=10126.552 E(PLAN)=331.159 | ------------------------------------------------------------------------------- --------------- cycle= 300 ------ stepsize= 0.0001 ----------------------- | Etotal =26037.677 grad(E)=15.543 E(BOND)=714.896 E(ANGL)=9963.008 | | E(VDW )=1838.183 E(CDIH)=3071.220 E(NOE )=10116.309 E(PLAN)=334.062 | ------------------------------------------------------------------------------- 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= 0.176232086E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : -0.07364 -0.03341 -0.23286 ang. mom. [amu A/ps] : -28059.73410-115853.92605 87878.53228 kin. ener. [Kcal/mol] : 4.91591 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 CODIMP: improper type-based parameters retrieved NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 728 exclusions and 0 interactions(1-4) NBONDS: found 12415 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=29570.087 E(kin)=5962.105 temperature=2954.473 | | Etotal =23607.982 grad(E)=73.258 E(BOND)=71.490 E(ANGL)=996.301 | | E(DIHE)=0.000 E(IMPR)=7180.418 E(VDW )=1838.183 E(CDIH)=3071.220 | | E(NOE )=10116.309 E(PLAN)=334.062 | ------------------------------------------------------------------------------- NBONDS: found 12455 intra-atom interactions NBONDS: found 12447 intra-atom interactions NBONDS: found 12404 intra-atom interactions NBONDS: found 12353 intra-atom interactions NBONDS: found 12316 intra-atom interactions NBONDS: found 12284 intra-atom interactions NBONDS: found 12222 intra-atom interactions NBONDS: found 12115 intra-atom interactions NBONDS: found 12084 intra-atom interactions NBONDS: found 12045 intra-atom interactions NBONDS: found 11977 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=26950.001 E(kin)=7321.371 temperature=3628.047 | | Etotal =19628.631 grad(E)=70.754 E(BOND)=2575.320 E(ANGL)=5041.583 | | E(DIHE)=0.000 E(IMPR)=3498.138 E(VDW )=883.002 E(CDIH)=1697.975 | | E(NOE )=5657.326 E(PLAN)=275.287 | ------------------------------------------------------------------------------- NBONDS: found 11973 intra-atom interactions NBONDS: found 11945 intra-atom interactions NBONDS: found 11877 intra-atom interactions NBONDS: found 11810 intra-atom interactions NBONDS: found 11736 intra-atom interactions NBONDS: found 11694 intra-atom interactions NBONDS: found 11634 intra-atom interactions NBONDS: found 11576 intra-atom interactions NBONDS: found 11485 intra-atom interactions NBONDS: found 11416 intra-atom interactions NBONDS: found 11399 intra-atom interactions NBONDS: found 11386 intra-atom interactions NBONDS: found 11349 intra-atom interactions NBONDS: found 11344 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=23226.686 E(kin)=7077.981 temperature=3507.437 | | Etotal =16148.705 grad(E)=63.985 E(BOND)=2513.076 E(ANGL)=4312.772 | | E(DIHE)=0.000 E(IMPR)=2287.243 E(VDW )=541.171 E(CDIH)=1842.731 | | E(NOE )=4423.597 E(PLAN)=228.114 | ------------------------------------------------------------------------------- NBONDS: found 11337 intra-atom interactions NBONDS: found 11298 intra-atom interactions NBONDS: found 11297 intra-atom interactions NBONDS: found 11263 intra-atom interactions NBONDS: found 11265 intra-atom interactions NBONDS: found 11179 intra-atom interactions NBONDS: found 11183 intra-atom interactions NBONDS: found 11188 intra-atom interactions NBONDS: found 11198 intra-atom interactions NBONDS: found 11194 intra-atom interactions NBONDS: found 11179 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=20432.548 E(kin)=6333.942 temperature=3138.734 | | Etotal =14098.607 grad(E)=62.384 E(BOND)=2489.386 E(ANGL)=3791.416 | | E(DIHE)=0.000 E(IMPR)=2036.587 E(VDW )=511.796 E(CDIH)=1286.195 | | E(NOE )=3761.449 E(PLAN)=221.778 | ------------------------------------------------------------------------------- NBONDS: found 11166 intra-atom interactions NBONDS: found 11161 intra-atom interactions NBONDS: found 11167 intra-atom interactions NBONDS: found 11116 intra-atom interactions NBONDS: found 11127 intra-atom interactions NBONDS: found 11107 intra-atom interactions NBONDS: found 11122 intra-atom interactions NBONDS: found 11103 intra-atom interactions NBONDS: found 11059 intra-atom interactions NBONDS: found 11006 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=19487.479 E(kin)=6288.112 temperature=3116.024 | | Etotal =13199.367 grad(E)=61.375 E(BOND)=2057.750 E(ANGL)=3946.452 | | E(DIHE)=0.000 E(IMPR)=1619.888 E(VDW )=442.164 E(CDIH)=1220.790 | | E(NOE )=3722.069 E(PLAN)=190.254 | ------------------------------------------------------------------------------- NBONDS: found 10956 intra-atom interactions NBONDS: found 10989 intra-atom interactions NBONDS: found 10931 intra-atom interactions NBONDS: found 10896 intra-atom interactions NBONDS: found 10893 intra-atom interactions NBONDS: found 10933 intra-atom interactions NBONDS: found 10903 intra-atom interactions NBONDS: found 10959 intra-atom interactions NBONDS: found 10963 intra-atom interactions NBONDS: found 10968 intra-atom interactions NBONDS: found 10966 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=18986.913 E(kin)=6518.194 temperature=3230.039 | | Etotal =12468.719 grad(E)=60.201 E(BOND)=2215.654 E(ANGL)=3385.071 | | E(DIHE)=0.000 E(IMPR)=1447.906 E(VDW )=507.705 E(CDIH)=963.040 | | E(NOE )=3715.808 E(PLAN)=233.536 | ------------------------------------------------------------------------------- NBONDS: found 10957 intra-atom interactions NBONDS: found 10903 intra-atom interactions NBONDS: found 10909 intra-atom interactions NBONDS: found 10873 intra-atom interactions NBONDS: found 10831 intra-atom interactions NBONDS: found 10884 intra-atom interactions NBONDS: found 10847 intra-atom interactions NBONDS: found 10860 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=18337.235 E(kin)=6103.517 temperature=3024.549 | | Etotal =12233.718 grad(E)=63.060 E(BOND)=2220.203 E(ANGL)=3209.942 | | E(DIHE)=0.000 E(IMPR)=1517.308 E(VDW )=528.371 E(CDIH)=860.306 | | E(NOE )=3611.538 E(PLAN)=286.051 | ------------------------------------------------------------------------------- NBONDS: found 10900 intra-atom interactions NBONDS: found 10951 intra-atom interactions NBONDS: found 10971 intra-atom interactions NBONDS: found 10956 intra-atom interactions NBONDS: found 10933 intra-atom interactions NBONDS: found 10924 intra-atom interactions NBONDS: found 10941 intra-atom interactions NBONDS: found 10941 intra-atom interactions NBONDS: found 10916 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=18321.768 E(kin)=6045.780 temperature=2995.938 | | Etotal =12275.988 grad(E)=60.961 E(BOND)=2052.093 E(ANGL)=3520.264 | | E(DIHE)=0.000 E(IMPR)=1281.584 E(VDW )=497.927 E(CDIH)=954.398 | | E(NOE )=3714.066 E(PLAN)=255.656 | ------------------------------------------------------------------------------- NBONDS: found 10887 intra-atom interactions NBONDS: found 10859 intra-atom interactions NBONDS: found 10808 intra-atom interactions NBONDS: found 10796 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> constraints inter (all) (all) weights * 0.2 dihe 0.1 impr 0.1 vdw 20 end end SELRPN: 677 atoms have been selected out of 677 SELRPN: 677 atoms have been selected out of 677 X-PLOR> dynamics verlet DYNAmics> nstep=$nstep1 time=$high_timestep iasvel=current firstt=$init_t DYNAmics> tcoup=true tbath=$init_t nprint=100 iprfrq=0 DYNAmics> end DYNAMC: number of degrees of freedom= 2031 ASSVEL: current velocities taken. CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 728 exclusions and 0 interactions(1-4) NBONDS: found 10780 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=24922.054 E(kin)=6166.630 temperature=3055.824 | | Etotal =18755.423 grad(E)=113.384 E(BOND)=4527.772 E(ANGL)=6480.058 | | E(DIHE)=0.000 E(IMPR)=2590.705 E(VDW )=527.757 E(CDIH)=812.251 | | E(NOE )=3514.413 E(PLAN)=302.467 | ------------------------------------------------------------------------------- NBONDS: found 10711 intra-atom interactions NBONDS: found 10689 intra-atom interactions NBONDS: found 10729 intra-atom interactions NBONDS: found 10736 intra-atom interactions NBONDS: found 10789 intra-atom interactions NBONDS: found 10835 intra-atom interactions NBONDS: found 10854 intra-atom interactions NBONDS: found 10842 intra-atom interactions NBONDS: found 10856 intra-atom interactions NBONDS: found 10847 intra-atom interactions NBONDS: found 10826 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=20618.871 E(kin)=6407.371 temperature=3175.121 | | Etotal =14211.500 grad(E)=86.898 E(BOND)=2630.006 E(ANGL)=3855.063 | | E(DIHE)=0.000 E(IMPR)=1825.544 E(VDW )=845.705 E(CDIH)=827.874 | | E(NOE )=4022.893 E(PLAN)=204.414 | ------------------------------------------------------------------------------- NBONDS: found 10831 intra-atom interactions NBONDS: found 10834 intra-atom interactions NBONDS: found 10828 intra-atom interactions NBONDS: found 10776 intra-atom interactions NBONDS: found 10751 intra-atom interactions NBONDS: found 10715 intra-atom interactions NBONDS: found 10728 intra-atom interactions NBONDS: found 10682 intra-atom interactions NBONDS: found 10674 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=19989.481 E(kin)=6167.705 temperature=3056.357 | | Etotal =13821.776 grad(E)=87.077 E(BOND)=2478.910 E(ANGL)=3801.271 | | E(DIHE)=0.000 E(IMPR)=1878.706 E(VDW )=729.417 E(CDIH)=759.681 | | E(NOE )=3894.036 E(PLAN)=279.754 | ------------------------------------------------------------------------------- NBONDS: found 10662 intra-atom interactions NBONDS: found 10648 intra-atom interactions NBONDS: found 10674 intra-atom interactions NBONDS: found 10699 intra-atom interactions NBONDS: found 10682 intra-atom interactions NBONDS: found 10695 intra-atom interactions NBONDS: found 10710 intra-atom interactions NBONDS: found 10705 intra-atom interactions NBONDS: found 10674 intra-atom interactions NBONDS: found 10693 intra-atom interactions NBONDS: found 10720 intra-atom interactions NBONDS: found 10732 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=19888.301 E(kin)=6282.000 temperature=3112.995 | | Etotal =13606.300 grad(E)=85.797 E(BOND)=2325.978 E(ANGL)=4224.310 | | E(DIHE)=0.000 E(IMPR)=1749.867 E(VDW )=649.571 E(CDIH)=519.856 | | E(NOE )=3928.291 E(PLAN)=208.429 | ------------------------------------------------------------------------------- NBONDS: found 10715 intra-atom interactions NBONDS: found 10746 intra-atom interactions NBONDS: found 10794 intra-atom interactions NBONDS: found 10808 intra-atom interactions NBONDS: found 10756 intra-atom interactions NBONDS: found 10760 intra-atom interactions NBONDS: found 10726 intra-atom interactions NBONDS: found 10695 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=19449.672 E(kin)=6242.396 temperature=3093.369 | | Etotal =13207.277 grad(E)=83.556 E(BOND)=2349.881 E(ANGL)=3940.626 | | E(DIHE)=0.000 E(IMPR)=1822.188 E(VDW )=555.371 E(CDIH)=439.810 | | E(NOE )=3884.588 E(PLAN)=214.813 | ------------------------------------------------------------------------------- NBONDS: found 10679 intra-atom interactions NBONDS: found 10664 intra-atom interactions NBONDS: found 10686 intra-atom interactions NBONDS: found 10791 intra-atom interactions NBONDS: found 10796 intra-atom interactions NBONDS: found 10793 intra-atom interactions NBONDS: found 10798 intra-atom interactions NBONDS: found 10827 intra-atom interactions NBONDS: found 10806 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=19336.498 E(kin)=6224.085 temperature=3084.295 | | Etotal =13112.413 grad(E)=87.429 E(BOND)=2589.342 E(ANGL)=3552.128 | | E(DIHE)=0.000 E(IMPR)=1873.002 E(VDW )=442.542 E(CDIH)=390.597 | | E(NOE )=3942.250 E(PLAN)=322.552 | ------------------------------------------------------------------------------- NBONDS: found 10794 intra-atom interactions NBONDS: found 10836 intra-atom interactions NBONDS: found 10908 intra-atom interactions NBONDS: found 10967 intra-atom interactions NBONDS: found 10961 intra-atom interactions NBONDS: found 10942 intra-atom interactions NBONDS: found 10911 intra-atom interactions NBONDS: found 10905 intra-atom interactions NBONDS: found 10945 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=19223.769 E(kin)=6118.325 temperature=3031.887 | | Etotal =13105.445 grad(E)=86.670 E(BOND)=2361.250 E(ANGL)=3949.664 | | E(DIHE)=0.000 E(IMPR)=1691.493 E(VDW )=507.301 E(CDIH)=445.151 | | E(NOE )=3849.993 E(PLAN)=300.594 | ------------------------------------------------------------------------------- NBONDS: found 10953 intra-atom interactions NBONDS: found 10954 intra-atom interactions NBONDS: found 11005 intra-atom interactions NBONDS: found 11051 intra-atom interactions NBONDS: found 11066 intra-atom interactions NBONDS: found 11118 intra-atom interactions NBONDS: found 11143 intra-atom interactions NBONDS: found 11178 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=19364.364 E(kin)=5962.543 temperature=2954.690 | | Etotal =13401.821 grad(E)=90.874 E(BOND)=2406.598 E(ANGL)=3908.759 | | E(DIHE)=0.000 E(IMPR)=1840.445 E(VDW )=522.445 E(CDIH)=417.181 | | E(NOE )=4017.772 E(PLAN)=288.622 | ------------------------------------------------------------------------------- NBONDS: found 11195 intra-atom interactions NBONDS: found 11242 intra-atom interactions NBONDS: found 11278 intra-atom interactions NBONDS: found 11246 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> constraints inter (all) (all) weights * 0.2 dihe 0.2 impr 0.2 vdw 0.01 end end SELRPN: 677 atoms have been selected out of 677 SELRPN: 677 atoms have been selected out of 677 X-PLOR> parameter nbonds repel=0.9 end end X-PLOR> dynamics verlet DYNAmics> nstep=$nstep1 time=$high_timestep iasvel=current firstt=$init_t DYNAmics> tcoup=true tbath=$init_t nprint=100 iprfrq=0 DYNAmics> end DYNAMC: number of degrees of freedom= 2031 ASSVEL: current velocities taken. CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 CODBON: bond type-based parameters retrieved CODANG: angle type-based parameters retrieved CODIMP: improper type-based parameters retrieved NBUPDA: type-based van der Waals parameters retrieved. NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 728 exclusions and 0 interactions(1-4) NBONDS: found 11234 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=20712.259 E(kin)=6189.808 temperature=3067.310 | | Etotal =14522.452 grad(E)=94.601 E(BOND)=2345.750 E(ANGL)=3868.392 | | E(DIHE)=0.000 E(IMPR)=3355.645 E(VDW )=335.872 E(CDIH)=409.796 | | E(NOE )=3913.527 E(PLAN)=293.469 | ------------------------------------------------------------------------------- NBONDS: found 11294 intra-atom interactions NBONDS: found 11425 intra-atom interactions NBONDS: found 11532 intra-atom interactions NBONDS: found 11636 intra-atom interactions NBONDS: found 11738 intra-atom interactions NBONDS: found 11865 intra-atom interactions NBONDS: found 11923 intra-atom interactions NBONDS: found 11908 intra-atom interactions NBONDS: found 11878 intra-atom interactions NBONDS: found 11895 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=19878.994 E(kin)=7098.978 temperature=3517.841 | | Etotal =12780.016 grad(E)=113.695 E(BOND)=2153.575 E(ANGL)=3634.803 | | E(DIHE)=0.000 E(IMPR)=1911.925 E(VDW )=410.903 E(CDIH)=492.040 | | E(NOE )=3924.721 E(PLAN)=252.050 | ------------------------------------------------------------------------------- NBONDS: found 11904 intra-atom interactions NBONDS: found 11875 intra-atom interactions NBONDS: found 11869 intra-atom interactions NBONDS: found 11890 intra-atom interactions NBONDS: found 11860 intra-atom interactions NBONDS: found 11862 intra-atom interactions NBONDS: found 11928 intra-atom interactions NBONDS: found 11999 intra-atom interactions NBONDS: found 12083 intra-atom interactions NBONDS: found 12095 intra-atom interactions NBONDS: found 12138 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=18585.834 E(kin)=6327.373 temperature=3135.479 | | Etotal =12258.462 grad(E)=90.933 E(BOND)=1964.619 E(ANGL)=3399.953 | | E(DIHE)=0.000 E(IMPR)=1731.476 E(VDW )=435.410 E(CDIH)=548.493 | | E(NOE )=3979.758 E(PLAN)=198.751 | ------------------------------------------------------------------------------- NBONDS: found 12191 intra-atom interactions NBONDS: found 12239 intra-atom interactions NBONDS: found 12235 intra-atom interactions NBONDS: found 12187 intra-atom interactions NBONDS: found 12207 intra-atom interactions NBONDS: found 12182 intra-atom interactions NBONDS: found 12221 intra-atom interactions NBONDS: found 12242 intra-atom interactions NBONDS: found 12231 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=18518.008 E(kin)=6447.653 temperature=3195.083 | | Etotal =12070.355 grad(E)=85.971 E(BOND)=1776.415 E(ANGL)=3518.907 | | E(DIHE)=0.000 E(IMPR)=1660.816 E(VDW )=420.813 E(CDIH)=701.885 | | E(NOE )=3753.182 E(PLAN)=238.338 | ------------------------------------------------------------------------------- NBONDS: found 12171 intra-atom interactions NBONDS: found 12148 intra-atom interactions NBONDS: found 12143 intra-atom interactions NBONDS: found 12155 intra-atom interactions NBONDS: found 12149 intra-atom interactions NBONDS: found 12115 intra-atom interactions NBONDS: found 12139 intra-atom interactions NBONDS: found 12204 intra-atom interactions NBONDS: found 12181 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=18113.872 E(kin)=6398.489 temperature=3170.720 | | Etotal =11715.383 grad(E)=89.920 E(BOND)=1925.087 E(ANGL)=3297.974 | | E(DIHE)=0.000 E(IMPR)=1479.192 E(VDW )=409.773 E(CDIH)=621.990 | | E(NOE )=3732.178 E(PLAN)=249.190 | ------------------------------------------------------------------------------- NBONDS: found 12193 intra-atom interactions NBONDS: found 12200 intra-atom interactions NBONDS: found 12183 intra-atom interactions NBONDS: found 12166 intra-atom interactions NBONDS: found 12170 intra-atom interactions NBONDS: found 12182 intra-atom interactions NBONDS: found 12192 intra-atom interactions NBONDS: found 12178 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=17627.669 E(kin)=5975.771 temperature=2961.245 | | Etotal =11651.898 grad(E)=93.419 E(BOND)=2167.401 E(ANGL)=3238.451 | | E(DIHE)=0.000 E(IMPR)=1190.038 E(VDW )=412.652 E(CDIH)=590.904 | | E(NOE )=3780.572 E(PLAN)=271.880 | ------------------------------------------------------------------------------- NBONDS: found 12216 intra-atom interactions NBONDS: found 12238 intra-atom interactions NBONDS: found 12315 intra-atom interactions NBONDS: found 12365 intra-atom interactions NBONDS: found 12414 intra-atom interactions NBONDS: found 12454 intra-atom interactions NBONDS: found 12486 intra-atom interactions NBONDS: found 12529 intra-atom interactions NBONDS: found 12591 intra-atom interactions NBONDS: found 12599 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=17628.458 E(kin)=6079.623 temperature=3012.709 | | Etotal =11548.835 grad(E)=91.193 E(BOND)=2032.941 E(ANGL)=3335.211 | | E(DIHE)=0.000 E(IMPR)=1220.785 E(VDW )=454.730 E(CDIH)=588.176 | | E(NOE )=3645.622 E(PLAN)=271.370 | ------------------------------------------------------------------------------- NBONDS: found 12658 intra-atom interactions NBONDS: found 12757 intra-atom interactions NBONDS: found 12776 intra-atom interactions NBONDS: found 12794 intra-atom interactions NBONDS: found 12848 intra-atom interactions NBONDS: found 12871 intra-atom interactions NBONDS: found 12895 intra-atom interactions NBONDS: found 12869 intra-atom interactions NBONDS: found 12962 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=17517.797 E(kin)=6112.641 temperature=3029.070 | | Etotal =11405.156 grad(E)=89.270 E(BOND)=2130.479 E(ANGL)=3302.054 | | E(DIHE)=0.000 E(IMPR)=1106.058 E(VDW )=469.698 E(CDIH)=447.327 | | E(NOE )=3636.307 E(PLAN)=313.231 | ------------------------------------------------------------------------------- NBONDS: found 13002 intra-atom interactions NBONDS: found 13044 intra-atom interactions NBONDS: found 13067 intra-atom interactions NBONDS: found 13167 intra-atom interactions NBONDS: found 13232 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> constraints inter (all) (all) weights * 0.4 dihe 0.4 impr 0.4 vdw 0.003 end end SELRPN: 677 atoms have been selected out of 677 SELRPN: 677 atoms have been selected out of 677 X-PLOR> parameter nbonds nbxmod=-3 end end X-PLOR> dynamics verlet DYNAmics> nstep=$nstep2 time=$high_timestep iasvel=current firstt=$init_t DYNAmics> tcoup=true tbath=$init_t nprint=100 iprfrq=0 DYNAmics> end DYNAMC: number of degrees of freedom= 2031 ASSVEL: current velocities taken. CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 CODBON: bond type-based parameters retrieved CODANG: angle type-based parameters retrieved CODIMP: improper type-based parameters retrieved NBUPDA: type-based van der Waals parameters retrieved. NBONDS: generating intra-molecular exclusion list with mode=-3 MAKINB: mode -3 found 2027 exclusions and 0 interactions(1-4) NBONDS: found 11992 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=23427.006 E(kin)=6036.332 temperature=2991.256 | | Etotal =17390.674 grad(E)=177.289 E(BOND)=4213.299 E(ANGL)=6284.325 | | E(DIHE)=0.000 E(IMPR)=2347.123 E(VDW )=91.217 E(CDIH)=507.849 | | E(NOE )=3654.567 E(PLAN)=292.295 | ------------------------------------------------------------------------------- NBONDS: found 12112 intra-atom interactions NBONDS: found 12186 intra-atom interactions NBONDS: found 12239 intra-atom interactions NBONDS: found 12309 intra-atom interactions NBONDS: found 12313 intra-atom interactions NBONDS: found 12342 intra-atom interactions NBONDS: found 12470 intra-atom interactions NBONDS: found 12589 intra-atom interactions NBONDS: found 12636 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=19724.564 E(kin)=6433.182 temperature=3187.912 | | Etotal =13291.382 grad(E)=133.571 E(BOND)=2234.411 E(ANGL)=4343.376 | | E(DIHE)=0.000 E(IMPR)=1285.364 E(VDW )=105.713 E(CDIH)=555.649 | | E(NOE )=4499.571 E(PLAN)=267.299 | ------------------------------------------------------------------------------- NBONDS: found 12639 intra-atom interactions NBONDS: found 12641 intra-atom interactions NBONDS: found 12651 intra-atom interactions NBONDS: found 12730 intra-atom interactions NBONDS: found 12775 intra-atom interactions NBONDS: found 12755 intra-atom interactions NBONDS: found 12761 intra-atom interactions NBONDS: found 12790 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=18995.250 E(kin)=6153.200 temperature=3049.169 | | Etotal =12842.050 grad(E)=126.477 E(BOND)=2298.497 E(ANGL)=4075.687 | | E(DIHE)=0.000 E(IMPR)=1251.344 E(VDW )=108.522 E(CDIH)=687.075 | | E(NOE )=4176.995 E(PLAN)=243.930 | ------------------------------------------------------------------------------- NBONDS: found 12772 intra-atom interactions NBONDS: found 12739 intra-atom interactions NBONDS: found 12745 intra-atom interactions NBONDS: found 12718 intra-atom interactions NBONDS: found 12685 intra-atom interactions NBONDS: found 12677 intra-atom interactions NBONDS: found 12610 intra-atom interactions NBONDS: found 12573 intra-atom interactions NBONDS: found 12608 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=18829.793 E(kin)=6151.156 temperature=3048.156 | | Etotal =12678.638 grad(E)=129.143 E(BOND)=2193.546 E(ANGL)=3938.890 | | E(DIHE)=0.000 E(IMPR)=1159.148 E(VDW )=108.501 E(CDIH)=563.264 | | E(NOE )=4487.713 E(PLAN)=227.575 | ------------------------------------------------------------------------------- NBONDS: found 12587 intra-atom interactions NBONDS: found 12616 intra-atom interactions NBONDS: found 12602 intra-atom interactions NBONDS: found 12587 intra-atom interactions NBONDS: found 12591 intra-atom interactions NBONDS: found 12574 intra-atom interactions NBONDS: found 12568 intra-atom interactions NBONDS: found 12612 intra-atom interactions NBONDS: found 12607 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=18962.889 E(kin)=5993.870 temperature=2970.214 | | Etotal =12969.019 grad(E)=126.001 E(BOND)=2219.675 E(ANGL)=4187.597 | | E(DIHE)=0.000 E(IMPR)=1112.533 E(VDW )=113.029 E(CDIH)=658.624 | | E(NOE )=4483.453 E(PLAN)=194.108 | ------------------------------------------------------------------------------- NBONDS: found 12560 intra-atom interactions NBONDS: found 12539 intra-atom interactions NBONDS: found 12562 intra-atom interactions NBONDS: found 12582 intra-atom interactions NBONDS: found 12576 intra-atom interactions NBONDS: found 12487 intra-atom interactions NBONDS: found 12427 intra-atom interactions NBONDS: found 12364 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=19054.155 E(kin)=6154.682 temperature=3049.904 | | Etotal =12899.472 grad(E)=127.172 E(BOND)=2168.352 E(ANGL)=4162.885 | | E(DIHE)=0.000 E(IMPR)=1118.497 E(VDW )=101.053 E(CDIH)=689.929 | | E(NOE )=4451.689 E(PLAN)=207.067 | ------------------------------------------------------------------------------- NBONDS: found 12263 intra-atom interactions NBONDS: found 12288 intra-atom interactions NBONDS: found 12307 intra-atom interactions NBONDS: found 12287 intra-atom interactions NBONDS: found 12223 intra-atom interactions NBONDS: found 12204 intra-atom interactions NBONDS: found 12155 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=19099.957 E(kin)=6060.004 temperature=3002.986 | | Etotal =13039.953 grad(E)=128.097 E(BOND)=2091.056 E(ANGL)=4251.895 | | E(DIHE)=0.000 E(IMPR)=1254.434 E(VDW )=96.619 E(CDIH)=783.996 | | E(NOE )=4365.230 E(PLAN)=196.724 | ------------------------------------------------------------------------------- NBONDS: found 12097 intra-atom interactions NBONDS: found 12104 intra-atom interactions NBONDS: found 12108 intra-atom interactions NBONDS: found 12088 intra-atom interactions NBONDS: found 12012 intra-atom interactions NBONDS: found 11981 intra-atom interactions NBONDS: found 11928 intra-atom interactions NBONDS: found 11859 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=19063.370 E(kin)=6069.587 temperature=3007.735 | | Etotal =12993.783 grad(E)=130.874 E(BOND)=2260.337 E(ANGL)=4089.567 | | E(DIHE)=0.000 E(IMPR)=1172.859 E(VDW )=88.514 E(CDIH)=688.930 | | E(NOE )=4518.179 E(PLAN)=175.398 | ------------------------------------------------------------------------------- NBONDS: found 11786 intra-atom interactions NBONDS: found 11768 intra-atom interactions NBONDS: found 11722 intra-atom interactions NBONDS: found 11701 intra-atom interactions NBONDS: found 11712 intra-atom interactions NBONDS: found 11693 intra-atom interactions NBONDS: found 11623 intra-atom interactions NBONDS: found 11612 intra-atom interactions --------------- step= 800 at 1.60000 ps -------------------------------- | E(kin)+E(total)=18911.933 E(kin)=6138.020 temperature=3041.647 | | Etotal =12773.913 grad(E)=126.230 E(BOND)=2248.275 E(ANGL)=3968.733 | | E(DIHE)=0.000 E(IMPR)=1097.617 E(VDW )=82.968 E(CDIH)=560.951 | | E(NOE )=4612.238 E(PLAN)=203.130 | ------------------------------------------------------------------------------- NBONDS: found 11501 intra-atom interactions NBONDS: found 11455 intra-atom interactions NBONDS: found 11345 intra-atom interactions NBONDS: found 11308 intra-atom interactions NBONDS: found 11234 intra-atom interactions NBONDS: found 11175 intra-atom interactions NBONDS: found 11172 intra-atom interactions NBONDS: found 11169 intra-atom interactions --------------- step= 900 at 1.80000 ps -------------------------------- | E(kin)+E(total)=18690.661 E(kin)=6101.004 temperature=3023.304 | | Etotal =12589.657 grad(E)=129.436 E(BOND)=2087.222 E(ANGL)=3890.291 | | E(DIHE)=0.000 E(IMPR)=1434.622 E(VDW )=76.075 E(CDIH)=576.790 | | E(NOE )=4359.965 E(PLAN)=164.692 | ------------------------------------------------------------------------------- NBONDS: found 11161 intra-atom interactions NBONDS: found 11085 intra-atom interactions NBONDS: found 11110 intra-atom interactions NBONDS: found 11044 intra-atom interactions NBONDS: found 10974 intra-atom interactions NBONDS: found 10928 intra-atom interactions NBONDS: found 10903 intra-atom interactions NBONDS: found 10860 intra-atom interactions NBONDS: found 10819 intra-atom interactions NBONDS: found 10760 intra-atom interactions NBONDS: found 10706 intra-atom interactions --------------- step= 1000 at 2.00000 ps -------------------------------- | E(kin)+E(total)=17053.578 E(kin)=6644.281 temperature=3292.520 | | Etotal =10409.297 grad(E)=118.633 E(BOND)=1918.120 E(ANGL)=3121.164 | | E(DIHE)=0.000 E(IMPR)=930.031 E(VDW )=70.444 E(CDIH)=671.837 | | E(NOE )=3563.778 E(PLAN)=133.923 | ------------------------------------------------------------------------------- NBONDS: found 10736 intra-atom interactions NBONDS: found 10744 intra-atom interactions NBONDS: found 10749 intra-atom interactions NBONDS: found 10808 intra-atom interactions NBONDS: found 10731 intra-atom interactions NBONDS: found 10679 intra-atom interactions NBONDS: found 10675 intra-atom interactions NBONDS: found 10666 intra-atom interactions NBONDS: found 10640 intra-atom interactions NBONDS: found 10651 intra-atom interactions NBONDS: found 10683 intra-atom interactions NBONDS: found 10709 intra-atom interactions NBONDS: found 10676 intra-atom interactions --------------- step= 1100 at 2.20000 ps -------------------------------- | E(kin)+E(total)=15997.599 E(kin)=6594.139 temperature=3267.673 | | Etotal =9403.460 grad(E)=112.990 E(BOND)=1679.224 E(ANGL)=3145.181 | | E(DIHE)=0.000 E(IMPR)=774.630 E(VDW )=65.320 E(CDIH)=433.348 | | E(NOE )=3162.738 E(PLAN)=143.019 | ------------------------------------------------------------------------------- NBONDS: found 10666 intra-atom interactions NBONDS: found 10689 intra-atom interactions NBONDS: found 10684 intra-atom interactions NBONDS: found 10674 intra-atom interactions NBONDS: found 10614 intra-atom interactions NBONDS: found 10618 intra-atom interactions NBONDS: found 10578 intra-atom interactions NBONDS: found 10570 intra-atom interactions NBONDS: found 10605 intra-atom interactions NBONDS: found 10626 intra-atom interactions NBONDS: found 10613 intra-atom interactions NBONDS: found 10604 intra-atom interactions NBONDS: found 10591 intra-atom interactions NBONDS: found 10592 intra-atom interactions --------------- step= 1200 at 2.40000 ps -------------------------------- | E(kin)+E(total)=15352.997 E(kin)=6012.619 temperature=2979.505 | | Etotal =9340.378 grad(E)=116.288 E(BOND)=1728.328 E(ANGL)=3225.059 | | E(DIHE)=0.000 E(IMPR)=880.620 E(VDW )=64.781 E(CDIH)=347.706 | | E(NOE )=2954.684 E(PLAN)=139.198 | ------------------------------------------------------------------------------- NBONDS: found 10631 intra-atom interactions NBONDS: found 10633 intra-atom interactions NBONDS: found 10630 intra-atom interactions NBONDS: found 10655 intra-atom interactions NBONDS: found 10657 intra-atom interactions NBONDS: found 10646 intra-atom interactions NBONDS: found 10600 intra-atom interactions NBONDS: found 10602 intra-atom interactions NBONDS: found 10579 intra-atom interactions NBONDS: found 10614 intra-atom interactions NBONDS: found 10649 intra-atom interactions NBONDS: found 10694 intra-atom interactions NBONDS: found 10733 intra-atom interactions --------------- step= 1300 at 2.60000 ps -------------------------------- | E(kin)+E(total)=15954.696 E(kin)=6244.287 temperature=3094.306 | | Etotal =9710.409 grad(E)=124.732 E(BOND)=2049.240 E(ANGL)=3117.604 | | E(DIHE)=0.000 E(IMPR)=914.672 E(VDW )=63.333 E(CDIH)=325.223 | | E(NOE )=3098.821 E(PLAN)=141.517 | ------------------------------------------------------------------------------- NBONDS: found 10737 intra-atom interactions NBONDS: found 10758 intra-atom interactions NBONDS: found 10765 intra-atom interactions NBONDS: found 10750 intra-atom interactions NBONDS: found 10769 intra-atom interactions NBONDS: found 10791 intra-atom interactions NBONDS: found 10825 intra-atom interactions NBONDS: found 10840 intra-atom interactions NBONDS: found 10841 intra-atom interactions NBONDS: found 10796 intra-atom interactions NBONDS: found 10770 intra-atom interactions NBONDS: found 10738 intra-atom interactions NBONDS: found 10766 intra-atom interactions --------------- step= 1400 at 2.80000 ps -------------------------------- | E(kin)+E(total)=15509.914 E(kin)=6239.089 temperature=3091.731 | | Etotal =9270.825 grad(E)=120.066 E(BOND)=1987.714 E(ANGL)=3015.985 | | E(DIHE)=0.000 E(IMPR)=891.547 E(VDW )=61.249 E(CDIH)=340.891 | | E(NOE )=2842.003 E(PLAN)=131.434 | ------------------------------------------------------------------------------- NBONDS: found 10773 intra-atom interactions NBONDS: found 10777 intra-atom interactions NBONDS: found 10794 intra-atom interactions NBONDS: found 10806 intra-atom interactions NBONDS: found 10840 intra-atom interactions NBONDS: found 10813 intra-atom interactions NBONDS: found 10773 intra-atom interactions NBONDS: found 10774 intra-atom interactions NBONDS: found 10778 intra-atom interactions NBONDS: found 10769 intra-atom interactions NBONDS: found 10702 intra-atom interactions NBONDS: found 10717 intra-atom interactions --------------- step= 1500 at 3.00000 ps -------------------------------- | E(kin)+E(total)=15608.680 E(kin)=5987.484 temperature=2967.050 | | Etotal =9621.196 grad(E)=120.420 E(BOND)=1898.236 E(ANGL)=3242.048 | | E(DIHE)=0.000 E(IMPR)=935.665 E(VDW )=60.280 E(CDIH)=429.311 | | E(NOE )=2931.441 E(PLAN)=124.215 | ------------------------------------------------------------------------------- NBONDS: found 10767 intra-atom interactions NBONDS: found 10793 intra-atom interactions NBONDS: found 10783 intra-atom interactions NBONDS: found 10788 intra-atom interactions NBONDS: found 10771 intra-atom interactions NBONDS: found 10781 intra-atom interactions NBONDS: found 10761 intra-atom interactions NBONDS: found 10798 intra-atom interactions NBONDS: found 10733 intra-atom interactions NBONDS: found 10769 intra-atom interactions NBONDS: found 10751 intra-atom interactions --------------- step= 1600 at 3.20000 ps -------------------------------- | E(kin)+E(total)=15816.169 E(kin)=5576.901 temperature=2763.589 | | Etotal =10239.267 grad(E)=124.629 E(BOND)=2297.965 E(ANGL)=3442.072 | | E(DIHE)=0.000 E(IMPR)=951.136 E(VDW )=61.254 E(CDIH)=397.302 | | E(NOE )=2932.667 E(PLAN)=156.872 | ------------------------------------------------------------------------------- NBONDS: found 10717 intra-atom interactions NBONDS: found 10744 intra-atom interactions NBONDS: found 10748 intra-atom interactions NBONDS: found 10707 intra-atom interactions NBONDS: found 10722 intra-atom interactions NBONDS: found 10726 intra-atom interactions NBONDS: found 10717 intra-atom interactions NBONDS: found 10741 intra-atom interactions NBONDS: found 10738 intra-atom interactions NBONDS: found 10691 intra-atom interactions NBONDS: found 10688 intra-atom interactions --------------- step= 1700 at 3.40000 ps -------------------------------- | E(kin)+E(total)=15749.465 E(kin)=6126.751 temperature=3036.062 | | Etotal =9622.714 grad(E)=124.465 E(BOND)=2010.289 E(ANGL)=3454.683 | | E(DIHE)=0.000 E(IMPR)=910.037 E(VDW )=61.669 E(CDIH)=344.523 | | E(NOE )=2690.581 E(PLAN)=150.933 | ------------------------------------------------------------------------------- NBONDS: found 10665 intra-atom interactions NBONDS: found 10660 intra-atom interactions NBONDS: found 10643 intra-atom interactions NBONDS: found 10602 intra-atom interactions NBONDS: found 10579 intra-atom interactions NBONDS: found 10496 intra-atom interactions NBONDS: found 10435 intra-atom interactions NBONDS: found 10399 intra-atom interactions NBONDS: found 10374 intra-atom interactions NBONDS: found 10379 intra-atom interactions NBONDS: found 10346 intra-atom interactions --------------- step= 1800 at 3.60000 ps -------------------------------- | E(kin)+E(total)=15676.509 E(kin)=6185.412 temperature=3065.131 | | Etotal =9491.096 grad(E)=125.234 E(BOND)=2033.213 E(ANGL)=3323.985 | | E(DIHE)=0.000 E(IMPR)=876.751 E(VDW )=57.790 E(CDIH)=316.495 | | E(NOE )=2758.378 E(PLAN)=124.485 | ------------------------------------------------------------------------------- NBONDS: found 10365 intra-atom interactions NBONDS: found 10366 intra-atom interactions NBONDS: found 10419 intra-atom interactions NBONDS: found 10508 intra-atom interactions NBONDS: found 10471 intra-atom interactions NBONDS: found 10448 intra-atom interactions NBONDS: found 10507 intra-atom interactions NBONDS: found 10515 intra-atom interactions NBONDS: found 10527 intra-atom interactions --------------- step= 1900 at 3.80000 ps -------------------------------- | E(kin)+E(total)=15674.677 E(kin)=6248.188 temperature=3096.239 | | Etotal =9426.490 grad(E)=124.002 E(BOND)=2005.093 E(ANGL)=3136.987 | | E(DIHE)=0.000 E(IMPR)=826.848 E(VDW )=60.225 E(CDIH)=322.059 | | E(NOE )=2950.750 E(PLAN)=124.528 | ------------------------------------------------------------------------------- NBONDS: found 10539 intra-atom interactions NBONDS: found 10527 intra-atom interactions NBONDS: found 10537 intra-atom interactions NBONDS: found 10504 intra-atom interactions NBONDS: found 10459 intra-atom interactions NBONDS: found 10424 intra-atom interactions NBONDS: found 10378 intra-atom interactions NBONDS: found 10404 intra-atom interactions NBONDS: found 10405 intra-atom interactions --------------- step= 2000 at 4.00000 ps -------------------------------- | E(kin)+E(total)=15694.559 E(kin)=5895.134 temperature=2921.287 | | Etotal =9799.424 grad(E)=127.885 E(BOND)=2178.127 E(ANGL)=3216.963 | | E(DIHE)=0.000 E(IMPR)=916.284 E(VDW )=58.095 E(CDIH)=388.948 | | E(NOE )=2921.591 E(PLAN)=119.415 | ------------------------------------------------------------------------------- NBONDS: found 10334 intra-atom interactions NBONDS: found 10253 intra-atom interactions NBONDS: found 10190 intra-atom interactions NBONDS: found 10143 intra-atom interactions NBONDS: found 10194 intra-atom interactions NBONDS: found 10201 intra-atom interactions NBONDS: found 10175 intra-atom interactions NBONDS: found 10133 intra-atom interactions --------------- step= 2100 at 4.20000 ps -------------------------------- | E(kin)+E(total)=15729.288 E(kin)=6223.236 temperature=3083.875 | | Etotal =9506.052 grad(E)=118.341 E(BOND)=1962.706 E(ANGL)=3304.989 | | E(DIHE)=0.000 E(IMPR)=874.512 E(VDW )=57.512 E(CDIH)=404.030 | | E(NOE )=2782.129 E(PLAN)=120.174 | ------------------------------------------------------------------------------- NBONDS: found 10111 intra-atom interactions NBONDS: found 10093 intra-atom interactions NBONDS: found 10099 intra-atom interactions NBONDS: found 10061 intra-atom interactions NBONDS: found 10053 intra-atom interactions NBONDS: found 10038 intra-atom interactions NBONDS: found 10043 intra-atom interactions NBONDS: found 10033 intra-atom interactions NBONDS: found 10013 intra-atom interactions --------------- step= 2200 at 4.40000 ps -------------------------------- | E(kin)+E(total)=15904.794 E(kin)=6279.280 temperature=3111.647 | | Etotal =9625.513 grad(E)=125.378 E(BOND)=1928.311 E(ANGL)=3329.619 | | E(DIHE)=0.000 E(IMPR)=911.582 E(VDW )=55.727 E(CDIH)=357.773 | | E(NOE )=2924.808 E(PLAN)=117.693 | ------------------------------------------------------------------------------- NBONDS: found 10029 intra-atom interactions NBONDS: found 10049 intra-atom interactions NBONDS: found 10111 intra-atom interactions NBONDS: found 10097 intra-atom interactions NBONDS: found 10030 intra-atom interactions NBONDS: found 10030 intra-atom interactions NBONDS: found 10040 intra-atom interactions --------------- step= 2300 at 4.60000 ps -------------------------------- | E(kin)+E(total)=15773.205 E(kin)=6226.389 temperature=3085.437 | | Etotal =9546.816 grad(E)=124.790 E(BOND)=1888.304 E(ANGL)=3243.219 | | E(DIHE)=0.000 E(IMPR)=906.121 E(VDW )=58.879 E(CDIH)=417.238 | | E(NOE )=2864.901 E(PLAN)=168.153 | ------------------------------------------------------------------------------- NBONDS: found 10107 intra-atom interactions NBONDS: found 10118 intra-atom interactions NBONDS: found 10101 intra-atom interactions NBONDS: found 9994 intra-atom interactions NBONDS: found 9972 intra-atom interactions NBONDS: found 9953 intra-atom interactions NBONDS: found 9996 intra-atom interactions NBONDS: found 10016 intra-atom interactions --------------- step= 2400 at 4.80000 ps -------------------------------- | E(kin)+E(total)=15665.795 E(kin)=6165.839 temperature=3055.432 | | Etotal =9499.956 grad(E)=123.976 E(BOND)=1820.380 E(ANGL)=3510.049 | | E(DIHE)=0.000 E(IMPR)=838.730 E(VDW )=56.163 E(CDIH)=310.516 | | E(NOE )=2824.966 E(PLAN)=139.152 | ------------------------------------------------------------------------------- NBONDS: found 10054 intra-atom interactions NBONDS: found 10094 intra-atom interactions NBONDS: found 10044 intra-atom interactions NBONDS: found 10027 intra-atom interactions NBONDS: found 10008 intra-atom interactions NBONDS: found 9975 intra-atom interactions NBONDS: found 10065 intra-atom interactions NBONDS: found 10110 intra-atom interactions --------------- step= 2500 at 5.00000 ps -------------------------------- | E(kin)+E(total)=15727.239 E(kin)=6185.155 temperature=3065.004 | | Etotal =9542.084 grad(E)=121.902 E(BOND)=2075.638 E(ANGL)=3308.111 | | E(DIHE)=0.000 E(IMPR)=833.759 E(VDW )=57.705 E(CDIH)=308.101 | | E(NOE )=2814.133 E(PLAN)=144.638 | ------------------------------------------------------------------------------- NBONDS: found 10131 intra-atom interactions NBONDS: found 10172 intra-atom interactions NBONDS: found 10224 intra-atom interactions NBONDS: found 10306 intra-atom interactions NBONDS: found 10283 intra-atom interactions NBONDS: found 10236 intra-atom interactions NBONDS: found 10219 intra-atom interactions NBONDS: found 10256 intra-atom interactions NBONDS: found 10238 intra-atom interactions --------------- step= 2600 at 5.20000 ps -------------------------------- | E(kin)+E(total)=15842.960 E(kin)=6039.690 temperature=2992.920 | | Etotal =9803.270 grad(E)=127.713 E(BOND)=1982.973 E(ANGL)=3480.135 | | E(DIHE)=0.000 E(IMPR)=844.216 E(VDW )=58.355 E(CDIH)=326.211 | | E(NOE )=2981.496 E(PLAN)=129.882 | ------------------------------------------------------------------------------- NBONDS: found 10254 intra-atom interactions NBONDS: found 10210 intra-atom interactions NBONDS: found 10210 intra-atom interactions NBONDS: found 10146 intra-atom interactions NBONDS: found 10171 intra-atom interactions NBONDS: found 10017 intra-atom interactions NBONDS: found 10007 intra-atom interactions NBONDS: found 10008 intra-atom interactions --------------- step= 2700 at 5.40000 ps -------------------------------- | E(kin)+E(total)=15987.711 E(kin)=6236.911 temperature=3090.652 | | Etotal =9750.799 grad(E)=129.658 E(BOND)=2020.185 E(ANGL)=3501.485 | | E(DIHE)=0.000 E(IMPR)=946.172 E(VDW )=49.886 E(CDIH)=356.281 | | E(NOE )=2730.300 E(PLAN)=146.490 | ------------------------------------------------------------------------------- NBONDS: found 9943 intra-atom interactions NBONDS: found 9935 intra-atom interactions NBONDS: found 9929 intra-atom interactions NBONDS: found 9940 intra-atom interactions NBONDS: found 9958 intra-atom interactions NBONDS: found 9954 intra-atom interactions NBONDS: found 9952 intra-atom interactions NBONDS: found 9974 intra-atom interactions --------------- step= 2800 at 5.60000 ps -------------------------------- | E(kin)+E(total)=15766.673 E(kin)=6105.765 temperature=3025.663 | | Etotal =9660.908 grad(E)=125.538 E(BOND)=2099.392 E(ANGL)=3522.406 | | E(DIHE)=0.000 E(IMPR)=840.722 E(VDW )=48.719 E(CDIH)=341.925 | | E(NOE )=2664.009 E(PLAN)=143.734 | ------------------------------------------------------------------------------- NBONDS: found 10020 intra-atom interactions NBONDS: found 10032 intra-atom interactions NBONDS: found 10065 intra-atom interactions NBONDS: found 9993 intra-atom interactions NBONDS: found 9956 intra-atom interactions NBONDS: found 9939 intra-atom interactions NBONDS: found 9902 intra-atom interactions --------------- step= 2900 at 5.80000 ps -------------------------------- | E(kin)+E(total)=15723.664 E(kin)=6000.067 temperature=2973.285 | | Etotal =9723.597 grad(E)=128.599 E(BOND)=2246.090 E(ANGL)=3338.004 | | E(DIHE)=0.000 E(IMPR)=938.504 E(VDW )=51.034 E(CDIH)=304.537 | | E(NOE )=2722.993 E(PLAN)=122.435 | ------------------------------------------------------------------------------- NBONDS: found 9929 intra-atom interactions NBONDS: found 9934 intra-atom interactions NBONDS: found 10003 intra-atom interactions NBONDS: found 9942 intra-atom interactions NBONDS: found 9912 intra-atom interactions NBONDS: found 9912 intra-atom interactions NBONDS: found 9904 intra-atom interactions NBONDS: found 9903 intra-atom interactions --------------- step= 3000 at 6.00000 ps -------------------------------- | E(kin)+E(total)=15784.054 E(kin)=5807.305 temperature=2877.763 | | Etotal =9976.749 grad(E)=128.525 E(BOND)=2140.018 E(ANGL)=3415.733 | | E(DIHE)=0.000 E(IMPR)=1040.298 E(VDW )=52.223 E(CDIH)=346.086 | | E(NOE )=2824.276 E(PLAN)=158.114 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> constraints inter (all) (all) weights * 1 dihe 1 impr 1 vdw 0.003 end end SELRPN: 677 atoms have been selected out of 677 SELRPN: 677 atoms have been selected out of 677 X-PLOR> dynamics verlet DYNAmics> nstep=$nstep1 time=$high_timestep iasvel=current firstt=$init_t DYNAmics> tcoup=true tbath=$init_t nprint=100 iprfrq=0 DYNAmics> end DYNAMC: number of degrees of freedom= 2031 ASSVEL: current velocities taken. CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 NBONDS: generating intra-molecular exclusion list with mode=-3 MAKINB: mode -3 found 2027 exclusions and 0 interactions(1-4) NBONDS: found 9947 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=25678.128 E(kin)=5807.305 temperature=2877.763 | | Etotal =19870.824 grad(E)=314.643 E(BOND)=5350.046 E(ANGL)=8539.334 | | E(DIHE)=0.000 E(IMPR)=2600.745 E(VDW )=52.223 E(CDIH)=346.086 | | E(NOE )=2824.276 E(PLAN)=158.114 | ------------------------------------------------------------------------------- NBONDS: found 9955 intra-atom interactions NBONDS: found 10001 intra-atom interactions NBONDS: found 10021 intra-atom interactions NBONDS: found 9981 intra-atom interactions NBONDS: found 10013 intra-atom interactions NBONDS: found 10032 intra-atom interactions NBONDS: found 10085 intra-atom interactions NBONDS: found 10116 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=18693.790 E(kin)=6227.875 temperature=3086.174 | | Etotal =12465.915 grad(E)=217.341 E(BOND)=2553.381 E(ANGL)=4343.807 | | E(DIHE)=0.000 E(IMPR)=970.613 E(VDW )=55.202 E(CDIH)=403.630 | | E(NOE )=4027.933 E(PLAN)=111.348 | ------------------------------------------------------------------------------- NBONDS: found 10182 intra-atom interactions NBONDS: found 10303 intra-atom interactions NBONDS: found 10259 intra-atom interactions NBONDS: found 10311 intra-atom interactions NBONDS: found 10332 intra-atom interactions NBONDS: found 10388 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=17928.743 E(kin)=6020.022 temperature=2983.174 | | Etotal =11908.721 grad(E)=215.718 E(BOND)=2394.225 E(ANGL)=4036.070 | | E(DIHE)=0.000 E(IMPR)=1081.571 E(VDW )=56.078 E(CDIH)=396.292 | | E(NOE )=3783.874 E(PLAN)=160.613 | ------------------------------------------------------------------------------- NBONDS: found 10376 intra-atom interactions NBONDS: found 10319 intra-atom interactions NBONDS: found 10322 intra-atom interactions NBONDS: found 10297 intra-atom interactions NBONDS: found 10239 intra-atom interactions NBONDS: found 10239 intra-atom interactions NBONDS: found 10205 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=17713.984 E(kin)=6082.365 temperature=3014.067 | | Etotal =11631.618 grad(E)=209.978 E(BOND)=2293.016 E(ANGL)=3930.312 | | E(DIHE)=0.000 E(IMPR)=1000.662 E(VDW )=53.532 E(CDIH)=433.976 | | E(NOE )=3788.485 E(PLAN)=131.635 | ------------------------------------------------------------------------------- NBONDS: found 10123 intra-atom interactions NBONDS: found 10052 intra-atom interactions NBONDS: found 10092 intra-atom interactions NBONDS: found 10046 intra-atom interactions NBONDS: found 10054 intra-atom interactions NBONDS: found 10043 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=17674.177 E(kin)=6187.295 temperature=3066.065 | | Etotal =11486.882 grad(E)=203.631 E(BOND)=2184.205 E(ANGL)=3931.791 | | E(DIHE)=0.000 E(IMPR)=956.721 E(VDW )=52.648 E(CDIH)=411.336 | | E(NOE )=3781.407 E(PLAN)=168.774 | ------------------------------------------------------------------------------- NBONDS: found 10038 intra-atom interactions NBONDS: found 10049 intra-atom interactions NBONDS: found 10079 intra-atom interactions NBONDS: found 10104 intra-atom interactions NBONDS: found 10107 intra-atom interactions NBONDS: found 10126 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=17695.308 E(kin)=5743.446 temperature=2846.119 | | Etotal =11951.862 grad(E)=212.485 E(BOND)=2333.313 E(ANGL)=4202.988 | | E(DIHE)=0.000 E(IMPR)=1146.153 E(VDW )=53.443 E(CDIH)=372.364 | | E(NOE )=3714.213 E(PLAN)=129.389 | ------------------------------------------------------------------------------- NBONDS: found 10171 intra-atom interactions NBONDS: found 10208 intra-atom interactions NBONDS: found 10187 intra-atom interactions NBONDS: found 10157 intra-atom interactions NBONDS: found 10129 intra-atom interactions NBONDS: found 10128 intra-atom interactions NBONDS: found 10102 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=17719.819 E(kin)=5894.929 temperature=2921.185 | | Etotal =11824.890 grad(E)=208.810 E(BOND)=2352.091 E(ANGL)=3810.249 | | E(DIHE)=0.000 E(IMPR)=1200.654 E(VDW )=54.247 E(CDIH)=427.662 | | E(NOE )=3828.401 E(PLAN)=151.587 | ------------------------------------------------------------------------------- NBONDS: found 10100 intra-atom interactions NBONDS: found 10078 intra-atom interactions NBONDS: found 10080 intra-atom interactions NBONDS: found 10121 intra-atom interactions NBONDS: found 10183 intra-atom interactions NBONDS: found 10261 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=17765.673 E(kin)=6075.553 temperature=3010.691 | | Etotal =11690.121 grad(E)=211.198 E(BOND)=2374.245 E(ANGL)=4197.651 | | E(DIHE)=0.000 E(IMPR)=999.068 E(VDW )=55.929 E(CDIH)=396.898 | | E(NOE )=3547.508 E(PLAN)=118.822 | ------------------------------------------------------------------------------- NBONDS: found 10344 intra-atom interactions NBONDS: found 10348 intra-atom interactions NBONDS: found 10365 intra-atom interactions NBONDS: found 10392 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> if ($image=1) then NEXTCD: condition evaluated as true X-PLOR> vector do (store7=x) (all) ! Store first image in stores. SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store8=y) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store9=z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store4=vx) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store5=vy) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store6=vz) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> end if X-PLOR> X-PLOR>end loop imag X-PLOR>for $image in (1 -1) loop imag FOR LOOP: symbol IMAGE set to -1.00000 (real) X-PLOR> X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates COOR>REMARK FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/dg.pdb" COOR>REMARK DATE:16-Aug-96 17:03:07 created by user: COOR>ATOM 1 P GUA 1 13.541 2.340 -8.461 1.00 0.00 A COOR>ATOM 2 O1P GUA 1 11.861 4.493 -9.451 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 = 2.5276 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6599 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2936 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1601 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.4211 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2066 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6452 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.4754 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.1832 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.3654 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.0413 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.3620 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.9468 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.3569 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.3943 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.3886 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8381 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1759 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.8464 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1113 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.8519 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 14602 intra-atom interactions NBONDS: found 14660 intra-atom interactions NBONDS: found 14807 intra-atom interactions NBONDS: found 14908 intra-atom interactions NBONDS: found 15086 intra-atom interactions NBONDS: found 15328 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0002 ----------------------- | Etotal =115544.410 grad(E)=416.177 E(BOND)=19252.504 E(VDW )=9216.375 | | E(CDIH)=4533.667 E(NOE )=81852.725 E(PLAN)=689.139 | ------------------------------------------------------------------------------- NBONDS: found 15433 intra-atom interactions NBONDS: found 15466 intra-atom interactions NBONDS: found 15471 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =64988.151 grad(E)=147.923 E(BOND)=3888.785 E(VDW )=7147.482 | | E(CDIH)=3380.239 E(NOE )=50023.569 E(PLAN)=548.076 | ------------------------------------------------------------------------------- NBONDS: found 15509 intra-atom interactions NBONDS: found 15545 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =47950.119 grad(E)=145.097 E(BOND)=2472.465 E(VDW )=5487.691 | | E(CDIH)=3594.676 E(NOE )=35987.249 E(PLAN)=408.038 | ------------------------------------------------------------------------------- NBONDS: found 15543 intra-atom interactions NBONDS: found 15564 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =38249.157 grad(E)=91.828 E(BOND)=1854.202 E(VDW )=4203.258 | | E(CDIH)=3012.535 E(NOE )=28819.617 E(PLAN)=359.544 | ------------------------------------------------------------------------------- NBONDS: found 15521 intra-atom interactions NBONDS: found 15558 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0002 ----------------------- | Etotal =32021.340 grad(E)=83.570 E(BOND)=1463.869 E(VDW )=3668.919 | | E(CDIH)=2599.914 E(NOE )=23952.568 E(PLAN)=336.070 | ------------------------------------------------------------------------------- NBONDS: found 15477 intra-atom interactions NBONDS: found 15465 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0002 ----------------------- | Etotal =27743.209 grad(E)=66.346 E(BOND)=1226.314 E(VDW )=3161.629 | | E(CDIH)=2239.032 E(NOE )=20757.760 E(PLAN)=358.474 | ------------------------------------------------------------------------------- NBONDS: found 15459 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =24046.403 grad(E)=61.511 E(BOND)=734.136 E(VDW )=2477.758 | | E(CDIH)=2245.512 E(NOE )=18240.025 E(PLAN)=348.972 | ------------------------------------------------------------------------------- NBONDS: found 15385 intra-atom interactions NBONDS: found 15246 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0002 ----------------------- | Etotal =21159.121 grad(E)=61.227 E(BOND)=804.165 E(VDW )=1724.103 | | E(CDIH)=1918.069 E(NOE )=16359.499 E(PLAN)=353.285 | ------------------------------------------------------------------------------- NBONDS: found 15211 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0000 ----------------------- | Etotal =19547.141 grad(E)=69.080 E(BOND)=579.966 E(VDW )=1437.407 | | E(CDIH)=1879.683 E(NOE )=15329.284 E(PLAN)=320.800 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =19492.735 grad(E)=71.919 E(BOND)=610.628 E(VDW )=1435.997 | | E(CDIH)=1812.963 E(NOE )=15313.052 E(PLAN)=320.095 | ------------------------------------------------------------------------------- --------------- cycle= 110 ------ stepsize= 0.0000 ----------------------- | Etotal =19561.024 grad(E)=71.914 E(BOND)=610.606 E(VDW )=1435.998 | | E(CDIH)=1881.261 E(NOE )=15313.063 E(PLAN)=320.096 | ------------------------------------------------------------------------------- --------------- cycle= 120 ------ stepsize= 0.0000 ----------------------- | Etotal =19492.727 grad(E)=71.918 E(BOND)=610.611 E(VDW )=1435.998 | | E(CDIH)=1812.962 E(NOE )=15313.060 E(PLAN)=320.095 | ------------------------------------------------------------------------------- --------------- cycle= 130 ------ stepsize= 0.0000 ----------------------- | Etotal =19492.726 grad(E)=71.918 E(BOND)=610.611 E(VDW )=1435.998 | | E(CDIH)=1812.962 E(NOE )=15313.061 E(PLAN)=320.095 | ------------------------------------------------------------------------------- --------------- cycle= 140 ------ stepsize= 0.0000 ----------------------- | Etotal =19492.726 grad(E)=71.918 E(BOND)=610.610 E(VDW )=1435.998 | | E(CDIH)=1812.962 E(NOE )=15313.061 E(PLAN)=320.096 | ------------------------------------------------------------------------------- %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 15228 intra-atom interactions NBONDS: found 15057 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =107835.878 grad(E)=366.166 E(BOND)=12731.208 E(ANGL)=68298.125 | | E(VDW )=3556.931 E(CDIH)=3357.913 E(NOE )=19292.469 E(PLAN)=599.232 | ------------------------------------------------------------------------------- NBONDS: found 14974 intra-atom interactions NBONDS: found 14969 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =74095.818 grad(E)=176.446 E(BOND)=4335.380 E(ANGL)=38587.876 | | E(VDW )=3928.582 E(CDIH)=3940.722 E(NOE )=22697.388 E(PLAN)=605.871 | ------------------------------------------------------------------------------- NBONDS: found 14901 intra-atom interactions NBONDS: found 14866 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =60987.954 grad(E)=131.726 E(BOND)=3036.150 E(ANGL)=26641.999 | | E(VDW )=3443.510 E(CDIH)=4126.564 E(NOE )=23126.413 E(PLAN)=613.318 | ------------------------------------------------------------------------------- NBONDS: found 14818 intra-atom interactions NBONDS: found 14763 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =53754.249 grad(E)=99.107 E(BOND)=2502.305 E(ANGL)=21200.851 | | E(VDW )=3127.159 E(CDIH)=4212.201 E(NOE )=22130.110 E(PLAN)=581.622 | ------------------------------------------------------------------------------- NBONDS: found 14661 intra-atom interactions NBONDS: found 14558 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =48767.683 grad(E)=114.660 E(BOND)=2305.210 E(ANGL)=17591.593 | | E(VDW )=2783.952 E(CDIH)=4332.920 E(NOE )=21207.463 E(PLAN)=546.544 | ------------------------------------------------------------------------------- NBONDS: found 14553 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =45072.082 grad(E)=72.326 E(BOND)=1757.805 E(ANGL)=15880.916 | | E(VDW )=2582.243 E(CDIH)=4124.568 E(NOE )=20212.243 E(PLAN)=514.307 | ------------------------------------------------------------------------------- NBONDS: found 14469 intra-atom interactions NBONDS: found 14346 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =42014.953 grad(E)=75.544 E(BOND)=1683.462 E(ANGL)=13915.690 | | E(VDW )=2335.745 E(CDIH)=4057.144 E(NOE )=19547.598 E(PLAN)=475.315 | ------------------------------------------------------------------------------- NBONDS: found 14307 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =39374.527 grad(E)=54.522 E(BOND)=1508.288 E(ANGL)=12267.304 | | E(VDW )=2172.459 E(CDIH)=3964.406 E(NOE )=19014.086 E(PLAN)=447.985 | ------------------------------------------------------------------------------- NBONDS: found 14190 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =37379.410 grad(E)=51.448 E(BOND)=1375.093 E(ANGL)=11362.804 | | E(VDW )=1997.686 E(CDIH)=3872.888 E(NOE )=18329.557 E(PLAN)=441.382 | ------------------------------------------------------------------------------- NBONDS: found 14134 intra-atom interactions NBONDS: found 14072 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =36047.614 grad(E)=40.917 E(BOND)=1230.271 E(ANGL)=10845.520 | | E(VDW )=1810.054 E(CDIH)=3787.670 E(NOE )=17923.497 E(PLAN)=450.602 | ------------------------------------------------------------------------------- NBONDS: found 14023 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0001 ----------------------- | Etotal =34959.581 grad(E)=41.937 E(BOND)=1165.030 E(ANGL)=10454.097 | | E(VDW )=1634.933 E(CDIH)=3758.294 E(NOE )=17499.416 E(PLAN)=447.810 | ------------------------------------------------------------------------------- NBONDS: found 13911 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0001 ----------------------- | Etotal =34081.585 grad(E)=42.039 E(BOND)=1083.127 E(ANGL)=10142.275 | | E(VDW )=1548.631 E(CDIH)=3685.216 E(NOE )=17194.934 E(PLAN)=427.402 | ------------------------------------------------------------------------------- NBONDS: found 13816 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0001 ----------------------- | Etotal =33379.580 grad(E)=33.971 E(BOND)=1056.064 E(ANGL)=9980.504 | | E(VDW )=1546.005 E(CDIH)=3644.203 E(NOE )=16748.705 E(PLAN)=404.100 | ------------------------------------------------------------------------------- NBONDS: found 13704 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0001 ----------------------- | Etotal =32760.653 grad(E)=31.276 E(BOND)=1070.689 E(ANGL)=9791.983 | | E(VDW )=1553.637 E(CDIH)=3615.559 E(NOE )=16346.632 E(PLAN)=382.154 | ------------------------------------------------------------------------------- NBONDS: found 13543 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =32178.171 grad(E)=33.274 E(BOND)=1082.226 E(ANGL)=9727.391 | | E(VDW )=1442.551 E(CDIH)=3585.420 E(NOE )=15976.930 E(PLAN)=363.652 | ------------------------------------------------------------------------------- --------------- cycle= 160 ------ stepsize= 0.0001 ----------------------- | Etotal =31589.477 grad(E)=34.946 E(BOND)=1103.831 E(ANGL)=9619.860 | | E(VDW )=1383.157 E(CDIH)=3505.043 E(NOE )=15633.853 E(PLAN)=343.731 | ------------------------------------------------------------------------------- NBONDS: found 13364 intra-atom interactions --------------- cycle= 170 ------ stepsize= 0.0001 ----------------------- | Etotal =31041.503 grad(E)=29.655 E(BOND)=1039.635 E(ANGL)=9410.634 | | E(VDW )=1391.773 E(CDIH)=3441.197 E(NOE )=15433.082 E(PLAN)=325.182 | ------------------------------------------------------------------------------- NBONDS: found 13177 intra-atom interactions --------------- cycle= 180 ------ stepsize= 0.0001 ----------------------- | Etotal =30541.175 grad(E)=27.286 E(BOND)=980.156 E(ANGL)=9300.103 | | E(VDW )=1405.433 E(CDIH)=3427.099 E(NOE )=15111.694 E(PLAN)=316.692 | ------------------------------------------------------------------------------- NBONDS: found 13034 intra-atom interactions --------------- cycle= 190 ------ stepsize= 0.0001 ----------------------- | Etotal =30034.066 grad(E)=25.756 E(BOND)=999.347 E(ANGL)=9215.031 | | E(VDW )=1338.876 E(CDIH)=3413.884 E(NOE )=14752.477 E(PLAN)=314.450 | ------------------------------------------------------------------------------- NBONDS: found 12899 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =29561.774 grad(E)=27.893 E(BOND)=962.850 E(ANGL)=9136.041 | | E(VDW )=1247.502 E(CDIH)=3427.087 E(NOE )=14459.859 E(PLAN)=328.434 | ------------------------------------------------------------------------------- NBONDS: found 12737 intra-atom interactions --------------- cycle= 210 ------ stepsize= 0.0001 ----------------------- | Etotal =28337.051 grad(E)=58.687 E(BOND)=1113.786 E(ANGL)=7934.636 | | E(VDW )=1192.222 E(CDIH)=3470.204 E(NOE )=14303.602 E(PLAN)=322.601 | ------------------------------------------------------------------------------- NBONDS: found 12673 intra-atom interactions --------------- cycle= 220 ------ stepsize= 0.0001 ----------------------- | Etotal =27428.271 grad(E)=35.884 E(BOND)=961.372 E(ANGL)=7588.777 | | E(VDW )=1111.629 E(CDIH)=3443.901 E(NOE )=14007.372 E(PLAN)=315.219 | ------------------------------------------------------------------------------- --------------- cycle= 230 ------ stepsize= 0.0001 ----------------------- | Etotal =26960.199 grad(E)=17.247 E(BOND)=915.063 E(ANGL)=7341.762 | | E(VDW )=1097.355 E(CDIH)=3402.352 E(NOE )=13894.551 E(PLAN)=309.116 | ------------------------------------------------------------------------------- --------------- cycle= 240 ------ stepsize= 0.0001 ----------------------- | Etotal =26648.946 grad(E)=21.996 E(BOND)=906.621 E(ANGL)=7153.188 | | E(VDW )=1087.709 E(CDIH)=3371.759 E(NOE )=13821.941 E(PLAN)=307.727 | ------------------------------------------------------------------------------- NBONDS: found 12665 intra-atom interactions --------------- cycle= 250 ------ stepsize= 0.0001 ----------------------- | Etotal =26391.173 grad(E)=18.735 E(BOND)=896.390 E(ANGL)=7135.745 | | E(VDW )=1073.423 E(CDIH)=3328.784 E(NOE )=13647.375 E(PLAN)=309.456 | ------------------------------------------------------------------------------- --------------- cycle= 260 ------ stepsize= 0.0001 ----------------------- | Etotal =26167.997 grad(E)=18.452 E(BOND)=858.728 E(ANGL)=7091.993 | | E(VDW )=1046.622 E(CDIH)=3297.489 E(NOE )=13565.143 E(PLAN)=308.022 | ------------------------------------------------------------------------------- NBONDS: found 12606 intra-atom interactions --------------- cycle= 270 ------ stepsize= 0.0001 ----------------------- | Etotal =25966.868 grad(E)=15.138 E(BOND)=833.833 E(ANGL)=7094.570 | | E(VDW )=1022.380 E(CDIH)=3266.929 E(NOE )=13439.006 E(PLAN)=310.151 | ------------------------------------------------------------------------------- NBONDS: found 12594 intra-atom interactions --------------- cycle= 280 ------ stepsize= 0.0001 ----------------------- | Etotal =25796.947 grad(E)=15.248 E(BOND)=835.707 E(ANGL)=7108.707 | | E(VDW )=1026.985 E(CDIH)=3230.937 E(NOE )=13282.086 E(PLAN)=312.525 | ------------------------------------------------------------------------------- --------------- cycle= 290 ------ stepsize= 0.0001 ----------------------- | Etotal =25666.677 grad(E)=15.793 E(BOND)=833.334 E(ANGL)=7075.926 | | E(VDW )=1002.920 E(CDIH)=3207.203 E(NOE )=13232.698 E(PLAN)=314.596 | ------------------------------------------------------------------------------- --------------- cycle= 300 ------ stepsize= 0.0001 ----------------------- | Etotal =25546.882 grad(E)=13.782 E(BOND)=819.843 E(ANGL)=7055.584 | | E(VDW )=971.103 E(CDIH)=3191.644 E(NOE )=13198.898 E(PLAN)=309.811 | ------------------------------------------------------------------------------- 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= 0.111465592E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.32434 -0.28550 -0.13055 ang. mom. [amu A/ps] : 78676.40797-215948.29499 -46450.50337 kin. ener. [Kcal/mol] : 16.48434 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 CODIMP: improper type-based parameters retrieved NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 728 exclusions and 0 interactions(1-4) NBONDS: found 12515 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=35503.184 E(kin)=6298.988 temperature=3121.413 | | Etotal =29204.195 grad(E)=78.345 E(BOND)=81.984 E(ANGL)=705.558 | | E(DIHE)=0.000 E(IMPR)=10745.197 E(VDW )=971.103 E(CDIH)=3191.644 | | E(NOE )=13198.898 E(PLAN)=309.811 | ------------------------------------------------------------------------------- NBONDS: found 12534 intra-atom interactions NBONDS: found 12468 intra-atom interactions NBONDS: found 12416 intra-atom interactions NBONDS: found 12396 intra-atom interactions NBONDS: found 12392 intra-atom interactions NBONDS: found 12351 intra-atom interactions NBONDS: found 12355 intra-atom interactions NBONDS: found 12303 intra-atom interactions NBONDS: found 12325 intra-atom interactions NBONDS: found 12262 intra-atom interactions NBONDS: found 12271 intra-atom interactions NBONDS: found 12244 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=32225.581 E(kin)=7280.688 temperature=3607.886 | | Etotal =24944.893 grad(E)=71.208 E(BOND)=2738.307 E(ANGL)=5182.907 | | E(DIHE)=0.000 E(IMPR)=5789.856 E(VDW )=417.834 E(CDIH)=1773.810 | | E(NOE )=8763.732 E(PLAN)=278.447 | ------------------------------------------------------------------------------- NBONDS: found 12232 intra-atom interactions NBONDS: found 12213 intra-atom interactions NBONDS: found 12202 intra-atom interactions NBONDS: found 12171 intra-atom interactions NBONDS: found 12157 intra-atom interactions NBONDS: found 12145 intra-atom interactions NBONDS: found 12105 intra-atom interactions NBONDS: found 12059 intra-atom interactions NBONDS: found 12002 intra-atom interactions NBONDS: found 11903 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=29557.831 E(kin)=6819.359 temperature=3379.279 | | Etotal =22738.472 grad(E)=65.321 E(BOND)=2731.012 E(ANGL)=4382.309 | | E(DIHE)=0.000 E(IMPR)=5493.091 E(VDW )=447.691 E(CDIH)=1462.708 | | E(NOE )=7863.142 E(PLAN)=358.518 | ------------------------------------------------------------------------------- NBONDS: found 11865 intra-atom interactions NBONDS: found 11811 intra-atom interactions NBONDS: found 11783 intra-atom interactions NBONDS: found 11750 intra-atom interactions NBONDS: found 11771 intra-atom interactions NBONDS: found 11735 intra-atom interactions NBONDS: found 11659 intra-atom interactions NBONDS: found 11581 intra-atom interactions NBONDS: found 11549 intra-atom interactions NBONDS: found 11506 intra-atom interactions NBONDS: found 11454 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=27714.033 E(kin)=6289.035 temperature=3116.481 | | Etotal =21424.999 grad(E)=65.376 E(BOND)=2603.337 E(ANGL)=4142.391 | | E(DIHE)=0.000 E(IMPR)=5355.504 E(VDW )=269.294 E(CDIH)=1332.086 | | E(NOE )=7489.926 E(PLAN)=232.461 | ------------------------------------------------------------------------------- NBONDS: found 11437 intra-atom interactions NBONDS: found 11386 intra-atom interactions NBONDS: found 11349 intra-atom interactions NBONDS: found 11343 intra-atom interactions NBONDS: found 11267 intra-atom interactions NBONDS: found 11196 intra-atom interactions NBONDS: found 11147 intra-atom interactions NBONDS: found 11072 intra-atom interactions NBONDS: found 11000 intra-atom interactions NBONDS: found 10959 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=26778.822 E(kin)=6399.055 temperature=3171.000 | | Etotal =20379.767 grad(E)=60.981 E(BOND)=2599.103 E(ANGL)=3890.512 | | E(DIHE)=0.000 E(IMPR)=5122.242 E(VDW )=229.458 E(CDIH)=1414.210 | | E(NOE )=6996.852 E(PLAN)=127.390 | ------------------------------------------------------------------------------- NBONDS: found 10925 intra-atom interactions NBONDS: found 10893 intra-atom interactions NBONDS: found 10846 intra-atom interactions NBONDS: found 10786 intra-atom interactions NBONDS: found 10730 intra-atom interactions NBONDS: found 10713 intra-atom interactions NBONDS: found 10744 intra-atom interactions NBONDS: found 10763 intra-atom interactions NBONDS: found 10757 intra-atom interactions NBONDS: found 10738 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=25903.753 E(kin)=6221.336 temperature=3082.933 | | Etotal =19682.417 grad(E)=63.506 E(BOND)=2606.765 E(ANGL)=3977.680 | | E(DIHE)=0.000 E(IMPR)=5290.214 E(VDW )=247.168 E(CDIH)=1489.855 | | E(NOE )=5852.472 E(PLAN)=218.264 | ------------------------------------------------------------------------------- NBONDS: found 10796 intra-atom interactions NBONDS: found 10824 intra-atom interactions NBONDS: found 10860 intra-atom interactions NBONDS: found 10869 intra-atom interactions NBONDS: found 10908 intra-atom interactions NBONDS: found 10927 intra-atom interactions NBONDS: found 10982 intra-atom interactions NBONDS: found 10963 intra-atom interactions NBONDS: found 10995 intra-atom interactions NBONDS: found 10976 intra-atom interactions NBONDS: found 10963 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=25731.353 E(kin)=6129.365 temperature=3037.358 | | Etotal =19601.988 grad(E)=65.896 E(BOND)=2526.059 E(ANGL)=3991.270 | | E(DIHE)=0.000 E(IMPR)=5017.922 E(VDW )=454.931 E(CDIH)=1236.696 | | E(NOE )=6188.981 E(PLAN)=186.128 | ------------------------------------------------------------------------------- NBONDS: found 11024 intra-atom interactions NBONDS: found 11086 intra-atom interactions NBONDS: found 11117 intra-atom interactions NBONDS: found 11084 intra-atom interactions NBONDS: found 11115 intra-atom interactions NBONDS: found 11130 intra-atom interactions NBONDS: found 11115 intra-atom interactions NBONDS: found 11153 intra-atom interactions NBONDS: found 11135 intra-atom interactions NBONDS: found 11129 intra-atom interactions NBONDS: found 11144 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=24890.372 E(kin)=6017.867 temperature=2982.106 | | Etotal =18872.506 grad(E)=65.792 E(BOND)=2293.737 E(ANGL)=3750.225 | | E(DIHE)=0.000 E(IMPR)=4718.395 E(VDW )=414.274 E(CDIH)=1366.220 | | E(NOE )=6163.934 E(PLAN)=165.720 | ------------------------------------------------------------------------------- NBONDS: found 11189 intra-atom interactions NBONDS: found 11217 intra-atom interactions NBONDS: found 11272 intra-atom interactions NBONDS: found 11311 intra-atom interactions NBONDS: found 11319 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> constraints inter (all) (all) weights * 0.2 dihe 0.1 impr 0.1 vdw 20 end end SELRPN: 677 atoms have been selected out of 677 SELRPN: 677 atoms have been selected out of 677 X-PLOR> dynamics verlet DYNAmics> nstep=$nstep1 time=$high_timestep iasvel=current firstt=$init_t DYNAmics> tcoup=true tbath=$init_t nprint=100 iprfrq=0 DYNAmics> end DYNAMC: number of degrees of freedom= 2031 ASSVEL: current velocities taken. CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00000 -0.00001 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 728 exclusions and 0 interactions(1-4) NBONDS: found 11295 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=35670.608 E(kin)=5844.422 temperature=2896.156 | | Etotal =29826.186 grad(E)=122.375 E(BOND)=4689.092 E(ANGL)=7603.618 | | E(DIHE)=0.000 E(IMPR)=9589.631 E(VDW )=286.555 E(CDIH)=1289.732 | | E(NOE )=6226.735 E(PLAN)=140.825 | ------------------------------------------------------------------------------- NBONDS: found 11305 intra-atom interactions NBONDS: found 11308 intra-atom interactions NBONDS: found 11232 intra-atom interactions NBONDS: found 11258 intra-atom interactions NBONDS: found 11258 intra-atom interactions NBONDS: found 11244 intra-atom interactions NBONDS: found 11224 intra-atom interactions NBONDS: found 11210 intra-atom interactions NBONDS: found 11228 intra-atom interactions NBONDS: found 11207 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=31344.882 E(kin)=6349.812 temperature=3146.599 | | Etotal =24995.070 grad(E)=93.141 E(BOND)=2500.720 E(ANGL)=4881.703 | | E(DIHE)=0.000 E(IMPR)=8845.664 E(VDW )=409.554 E(CDIH)=1489.102 | | E(NOE )=6643.523 E(PLAN)=224.805 | ------------------------------------------------------------------------------- NBONDS: found 11204 intra-atom interactions NBONDS: found 11144 intra-atom interactions NBONDS: found 11077 intra-atom interactions NBONDS: found 11092 intra-atom interactions NBONDS: found 11110 intra-atom interactions NBONDS: found 11121 intra-atom interactions NBONDS: found 11138 intra-atom interactions NBONDS: found 11140 intra-atom interactions NBONDS: found 11148 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=30299.323 E(kin)=6193.492 temperature=3069.135 | | Etotal =24105.831 grad(E)=88.942 E(BOND)=2411.915 E(ANGL)=4602.994 | | E(DIHE)=0.000 E(IMPR)=8666.468 E(VDW )=236.619 E(CDIH)=1372.432 | | E(NOE )=6588.550 E(PLAN)=226.854 | ------------------------------------------------------------------------------- NBONDS: found 11125 intra-atom interactions NBONDS: found 11112 intra-atom interactions NBONDS: found 11168 intra-atom interactions NBONDS: found 11194 intra-atom interactions NBONDS: found 11198 intra-atom interactions NBONDS: found 11208 intra-atom interactions NBONDS: found 11221 intra-atom interactions NBONDS: found 11260 intra-atom interactions NBONDS: found 11290 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=29893.009 E(kin)=6319.131 temperature=3131.395 | | Etotal =23573.878 grad(E)=82.784 E(BOND)=2105.873 E(ANGL)=4433.458 | | E(DIHE)=0.000 E(IMPR)=8705.198 E(VDW )=359.000 E(CDIH)=1455.329 | | E(NOE )=6399.853 E(PLAN)=115.165 | ------------------------------------------------------------------------------- NBONDS: found 11370 intra-atom interactions NBONDS: found 11342 intra-atom interactions NBONDS: found 11298 intra-atom interactions NBONDS: found 11274 intra-atom interactions NBONDS: found 11278 intra-atom interactions NBONDS: found 11295 intra-atom interactions NBONDS: found 11326 intra-atom interactions NBONDS: found 11365 intra-atom interactions NBONDS: found 11368 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=29524.928 E(kin)=5980.427 temperature=2963.553 | | Etotal =23544.501 grad(E)=87.709 E(BOND)=2364.293 E(ANGL)=4804.584 | | E(DIHE)=0.000 E(IMPR)=8252.240 E(VDW )=260.094 E(CDIH)=1450.479 | | E(NOE )=6245.031 E(PLAN)=167.780 | ------------------------------------------------------------------------------- NBONDS: found 11349 intra-atom interactions NBONDS: found 11343 intra-atom interactions NBONDS: found 11319 intra-atom interactions NBONDS: found 11278 intra-atom interactions NBONDS: found 11273 intra-atom interactions NBONDS: found 11310 intra-atom interactions NBONDS: found 11337 intra-atom interactions NBONDS: found 11308 intra-atom interactions NBONDS: found 11366 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=29381.454 E(kin)=6148.409 temperature=3046.795 | | Etotal =23233.045 grad(E)=84.947 E(BOND)=2528.587 E(ANGL)=4306.979 | | E(DIHE)=0.000 E(IMPR)=8565.578 E(VDW )=252.604 E(CDIH)=1490.162 | | E(NOE )=5951.508 E(PLAN)=137.628 | ------------------------------------------------------------------------------- NBONDS: found 11498 intra-atom interactions NBONDS: found 11498 intra-atom interactions NBONDS: found 11515 intra-atom interactions NBONDS