X-PLOR: V3.840 user: on: Alpha/OSF at: 16-Aug-96 18:41:42 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=96059.8100280762 SET> end ! Use 'xplor -s' X-PLOR> X-PLOR>set echo=off message=off end ! Normal use REMARKS FILENAME="/sgi/people/dcs/ws/xplor/italy2.4x/rsf.inp" REMARKS DATE:27-Apr-96 13:37:21 created by user: XPLOR: current counts (number in parenthesis is maximum) NATOM= 677(MAXA= 96000) NBOND= 728(MAXB= 96000) NTHETA= 1299(MAXT= 144000) NGRP= 218(MAXGRP= 96000) NPHI= 0(MAXP= 180000) NIMPHI= 461(MAXIMP= 96000) NDON= 68(MAXPAD= 24000) NACC= 105(MAXPAD= 24000) NNB= 63(MAXNB= 18000) NOE: allocating space for 1000 restraints. XREFIN: allocating space for 300 assignments. X-PLOR> X-PLOR>vector do (fbeta=10) (all) ! Friction coeff. for MD heatbath, in 1/ps. SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (mass=100) (all) ! Uniform heavy masses to speed MD. SELRPN: 677 atoms have been selected out of 677 X-PLOR> X-PLOR>noe ! Parameters for NOE effective energy term. NOE> ceiling=1000 NOE> averaging * cent NOE> potential * square NOE> sqconstant * 1 NOE> sqexponent * 2 NOE> scale * 100 ! Constant NOE scale throughout the protocol. NOE>end X-PLOR> X-PLOR>parameter ! Parameters for the repulsive energy term. PARRDR> nbonds NBDSET> repel=0.5 ! Initial value for repel--modified later. NBDSET> rexp=2 NBDSET> irexp=2 NBDSET> rcon=1 NBDSET> nbxmod=-2 ! Initial value for nbxmod--modified later. NBDSET> wmin=0.01 NBDSET> cutnb=4.5 NBDSET> ctonnb=2.99 NBDSET> ctofnb=3 NBDSET> tolerance=0.5 NBDSET> end PARRDR>end X-PLOR> X-PLOR>! Test for the correct enantiomer; if you want to bypass this test because X-PLOR>! the substructures were tested previously, simply remove the -1 from the X-PLOR>! next statement. X-PLOR> X-PLOR>for $image in (1 -1) loop imag FOR LOOP: symbol IMAGE set to 1.00000 (real) X-PLOR> X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @dg.pdb ! END in PDB file ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/dg.pdb opened. COOR>REMARK FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/dg.pdb" COOR>REMARK DATE:16-Aug-96 18:39:32 created by user: COOR>ATOM 1 P GUA 1 11.985 -3.989 8.809 1.00 0.00 A COOR>ATOM 2 O1P GUA 1 14.459 -6.228 5.905 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 = 3.0159 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.9339 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0175 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8652 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0537 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9818 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9270 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.2543 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.9265 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.2559 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.3958 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.0938 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.2049 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.9050 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.4962 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1320 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.5991 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8584 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.5746 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8760 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.5772 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 15374 intra-atom interactions NBONDS: found 15440 intra-atom interactions NBONDS: found 15481 intra-atom interactions NBONDS: found 15537 intra-atom interactions NBONDS: found 15620 intra-atom interactions NBONDS: found 15648 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0002 ----------------------- | Etotal =103110.704 grad(E)=307.879 E(BOND)=13649.583 E(VDW )=11634.365 | | E(CDIH)=4237.745 E(NOE )=73055.296 E(PLAN)=533.714 | ------------------------------------------------------------------------------- NBONDS: found 15697 intra-atom interactions NBONDS: found 15662 intra-atom interactions NBONDS: found 15675 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =57897.684 grad(E)=187.581 E(BOND)=4664.487 E(VDW )=7987.025 | | E(CDIH)=3133.839 E(NOE )=41807.199 E(PLAN)=305.133 | ------------------------------------------------------------------------------- NBONDS: found 15690 intra-atom interactions NBONDS: found 15663 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =41082.386 grad(E)=100.602 E(BOND)=1882.151 E(VDW )=5749.711 | | E(CDIH)=2704.177 E(NOE )=30559.537 E(PLAN)=186.810 | ------------------------------------------------------------------------------- NBONDS: found 15574 intra-atom interactions NBONDS: found 15499 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0002 ----------------------- | Etotal =32272.147 grad(E)=99.939 E(BOND)=1545.868 E(VDW )=4079.787 | | E(CDIH)=2101.478 E(NOE )=24300.225 E(PLAN)=244.790 | ------------------------------------------------------------------------------- NBONDS: found 15377 intra-atom interactions NBONDS: found 15284 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =26466.842 grad(E)=76.131 E(BOND)=1034.247 E(VDW )=2813.893 | | E(CDIH)=1479.050 E(NOE )=20863.211 E(PLAN)=276.441 | ------------------------------------------------------------------------------- NBONDS: found 15156 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =22492.333 grad(E)=51.200 E(BOND)=631.459 E(VDW )=1972.894 | | E(CDIH)=1257.743 E(NOE )=18336.284 E(PLAN)=293.953 | ------------------------------------------------------------------------------- NBONDS: found 15002 intra-atom interactions NBONDS: found 14624 intra-atom interactions NBONDS: found 14949 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0000 ----------------------- | Etotal =20634.248 grad(E)=62.861 E(BOND)=769.969 E(VDW )=1682.634 | | E(CDIH)=1278.024 E(NOE )=16624.709 E(PLAN)=278.912 | ------------------------------------------------------------------------------- NBONDS: found 14811 intra-atom interactions NBONDS: found 14688 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =18505.048 grad(E)=57.049 E(BOND)=583.522 E(VDW )=1351.864 | | E(CDIH)=1206.878 E(NOE )=15109.955 E(PLAN)=252.829 | ------------------------------------------------------------------------------- NBONDS: found 14559 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0000 ----------------------- | Etotal =17141.289 grad(E)=38.611 E(BOND)=413.279 E(VDW )=1302.085 | | E(CDIH)=1102.863 E(NOE )=14110.304 E(PLAN)=212.758 | ------------------------------------------------------------------------------- NBONDS: found 14438 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =16015.712 grad(E)=32.176 E(BOND)=343.292 E(VDW )=1084.115 | | E(CDIH)=847.614 E(NOE )=13521.634 E(PLAN)=219.057 | ------------------------------------------------------------------------------- NBONDS: found 14207 intra-atom interactions NBONDS: found 14375 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0000 ----------------------- | Etotal =15269.385 grad(E)=32.429 E(BOND)=288.460 E(VDW )=873.281 | | E(CDIH)=813.985 E(NOE )=13077.356 E(PLAN)=216.302 | ------------------------------------------------------------------------------- --------------- cycle= 120 ------ stepsize= 0.0000 ----------------------- | Etotal =14795.785 grad(E)=20.146 E(BOND)=227.024 E(VDW )=772.305 | | E(CDIH)=734.696 E(NOE )=12851.964 E(PLAN)=209.796 | ------------------------------------------------------------------------------- --------------- cycle= 130 ------ stepsize= 0.0000 ----------------------- | Etotal =14779.268 grad(E)=18.751 E(BOND)=223.025 E(VDW )=770.311 | | E(CDIH)=732.976 E(NOE )=12843.436 E(PLAN)=209.520 | ------------------------------------------------------------------------------- --------------- cycle= 140 ------ stepsize= 0.0000 ----------------------- | Etotal =14956.211 grad(E)=22.707 E(BOND)=222.994 E(VDW )=770.288 | | E(CDIH)=910.081 E(NOE )=12843.332 E(PLAN)=209.517 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =14779.089 grad(E)=18.740 E(BOND)=222.994 E(VDW )=770.288 | | E(CDIH)=732.956 E(NOE )=12843.334 E(PLAN)=209.517 | ------------------------------------------------------------------------------- --------------- cycle= 160 ------ stepsize= 0.0000 ----------------------- | Etotal =14779.089 grad(E)=18.740 E(BOND)=222.994 E(VDW )=770.288 | | E(CDIH)=732.956 E(NOE )=12843.334 E(PLAN)=209.517 | ------------------------------------------------------------------------------- %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 14348 intra-atom interactions NBONDS: found 14289 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =107646.730 grad(E)=351.648 E(BOND)=13994.601 E(ANGL)=71372.608 | | E(VDW )=2812.963 E(CDIH)=2182.896 E(NOE )=16914.566 E(PLAN)=369.095 | ------------------------------------------------------------------------------- NBONDS: found 14222 intra-atom interactions NBONDS: found 14231 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =71793.305 grad(E)=189.687 E(BOND)=5209.680 E(ANGL)=38367.841 | | E(VDW )=3340.452 E(CDIH)=2869.496 E(NOE )=21546.503 E(PLAN)=459.334 | ------------------------------------------------------------------------------- NBONDS: found 14241 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =58720.332 grad(E)=108.351 E(BOND)=3748.069 E(ANGL)=25955.403 | | E(VDW )=3347.017 E(CDIH)=3358.264 E(NOE )=21867.725 E(PLAN)=443.854 | ------------------------------------------------------------------------------- NBONDS: found 14195 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =51967.806 grad(E)=102.931 E(BOND)=2887.085 E(ANGL)=21698.834 | | E(VDW )=3271.691 E(CDIH)=3385.101 E(NOE )=20290.758 E(PLAN)=434.338 | ------------------------------------------------------------------------------- NBONDS: found 14116 intra-atom interactions NBONDS: found 13970 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =47223.838 grad(E)=84.314 E(BOND)=2178.645 E(ANGL)=18584.988 | | E(VDW )=2910.686 E(CDIH)=3369.777 E(NOE )=19732.285 E(PLAN)=447.458 | ------------------------------------------------------------------------------- NBONDS: found 13849 intra-atom interactions NBONDS: found 13647 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =43773.214 grad(E)=83.990 E(BOND)=1875.118 E(ANGL)=16206.018 | | E(VDW )=2818.636 E(CDIH)=3210.048 E(NOE )=19190.081 E(PLAN)=473.313 | ------------------------------------------------------------------------------- NBONDS: found 13499 intra-atom interactions NBONDS: found 13402 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =40306.306 grad(E)=85.224 E(BOND)=1998.579 E(ANGL)=13583.831 | | E(VDW )=2451.472 E(CDIH)=3086.466 E(NOE )=18747.416 E(PLAN)=438.542 | ------------------------------------------------------------------------------- NBONDS: found 13270 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =36793.274 grad(E)=62.330 E(BOND)=1797.090 E(ANGL)=10893.557 | | E(VDW )=2154.865 E(CDIH)=3040.899 E(NOE )=18497.002 E(PLAN)=409.860 | ------------------------------------------------------------------------------- NBONDS: found 13181 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =33964.668 grad(E)=73.995 E(BOND)=1577.377 E(ANGL)=9939.237 | | E(VDW )=1887.941 E(CDIH)=2920.953 E(NOE )=17242.057 E(PLAN)=397.103 | ------------------------------------------------------------------------------- NBONDS: found 13172 intra-atom interactions NBONDS: found 13137 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =31761.640 grad(E)=50.971 E(BOND)=1490.991 E(ANGL)=9578.501 | | E(VDW )=1468.833 E(CDIH)=2857.354 E(NOE )=15980.174 E(PLAN)=385.787 | ------------------------------------------------------------------------------- NBONDS: found 13081 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0001 ----------------------- | Etotal =30227.430 grad(E)=44.805 E(BOND)=1357.821 E(ANGL)=9357.984 | | E(VDW )=1275.056 E(CDIH)=2804.124 E(NOE )=15059.671 E(PLAN)=372.775 | ------------------------------------------------------------------------------- NBONDS: found 13043 intra-atom interactions NBONDS: found 12969 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0001 ----------------------- | Etotal =28876.035 grad(E)=41.584 E(BOND)=1242.929 E(ANGL)=9120.043 | | E(VDW )=1240.515 E(CDIH)=2579.720 E(NOE )=14345.891 E(PLAN)=346.937 | ------------------------------------------------------------------------------- --------------- cycle= 130 ------ stepsize= 0.0001 ----------------------- | Etotal =27803.036 grad(E)=32.584 E(BOND)=1149.383 E(ANGL)=8777.131 | | E(VDW )=1256.140 E(CDIH)=2502.229 E(NOE )=13802.025 E(PLAN)=316.128 | ------------------------------------------------------------------------------- NBONDS: found 12973 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0001 ----------------------- | Etotal =26989.904 grad(E)=35.152 E(BOND)=1159.159 E(ANGL)=8636.474 | | E(VDW )=1278.412 E(CDIH)=2452.902 E(NOE )=13167.616 E(PLAN)=295.342 | ------------------------------------------------------------------------------- NBONDS: found 12916 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =26258.815 grad(E)=41.445 E(BOND)=1044.510 E(ANGL)=8460.021 | | E(VDW )=1278.116 E(CDIH)=2403.104 E(NOE )=12789.271 E(PLAN)=283.791 | ------------------------------------------------------------------------------- NBONDS: found 12816 intra-atom interactions --------------- cycle= 160 ------ stepsize= 0.0001 ----------------------- | Etotal =25490.728 grad(E)=38.240 E(BOND)=1049.132 E(ANGL)=8182.246 | | E(VDW )=1222.052 E(CDIH)=2369.896 E(NOE )=12380.491 E(PLAN)=286.911 | ------------------------------------------------------------------------------- NBONDS: found 12709 intra-atom interactions --------------- cycle= 170 ------ stepsize= 0.0001 ----------------------- | Etotal =24546.127 grad(E)=41.034 E(BOND)=1018.854 E(ANGL)=7915.316 | | E(VDW )=1142.768 E(CDIH)=2316.622 E(NOE )=11834.765 E(PLAN)=317.802 | ------------------------------------------------------------------------------- NBONDS: found 12625 intra-atom interactions NBONDS: found 12548 intra-atom interactions --------------- cycle= 180 ------ stepsize= 0.0001 ----------------------- | Etotal =23482.131 grad(E)=41.246 E(BOND)=871.211 E(ANGL)=7598.719 | | E(VDW )=1144.336 E(CDIH)=2271.436 E(NOE )=11264.547 E(PLAN)=331.882 | ------------------------------------------------------------------------------- NBONDS: found 12507 intra-atom interactions --------------- cycle= 190 ------ stepsize= 0.0001 ----------------------- | Etotal =22571.574 grad(E)=39.672 E(BOND)=787.874 E(ANGL)=7242.324 | | E(VDW )=1106.373 E(CDIH)=2285.262 E(NOE )=10821.031 E(PLAN)=328.709 | ------------------------------------------------------------------------------- NBONDS: found 12498 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =21849.898 grad(E)=33.567 E(BOND)=752.682 E(ANGL)=6818.029 | | E(VDW )=1016.351 E(CDIH)=2287.400 E(NOE )=10643.333 E(PLAN)=332.102 | ------------------------------------------------------------------------------- NBONDS: found 12466 intra-atom interactions --------------- cycle= 210 ------ stepsize= 0.0001 ----------------------- | Etotal =21124.477 grad(E)=35.120 E(BOND)=752.324 E(ANGL)=6686.955 | | E(VDW )=981.074 E(CDIH)=2260.140 E(NOE )=10104.274 E(PLAN)=339.711 | ------------------------------------------------------------------------------- NBONDS: found 12425 intra-atom interactions --------------- cycle= 220 ------ stepsize= 0.0001 ----------------------- | Etotal =20497.691 grad(E)=29.997 E(BOND)=725.886 E(ANGL)=6523.706 | | E(VDW )=942.607 E(CDIH)=2241.254 E(NOE )=9736.536 E(PLAN)=327.703 | ------------------------------------------------------------------------------- NBONDS: found 12382 intra-atom interactions --------------- cycle= 230 ------ stepsize= 0.0001 ----------------------- | Etotal =19970.929 grad(E)=29.044 E(BOND)=699.997 E(ANGL)=6287.904 | | E(VDW )=892.881 E(CDIH)=2211.786 E(NOE )=9560.139 E(PLAN)=318.221 | ------------------------------------------------------------------------------- --------------- cycle= 240 ------ stepsize= 0.0001 ----------------------- | Etotal =19542.065 grad(E)=24.742 E(BOND)=678.665 E(ANGL)=6125.102 | | E(VDW )=855.748 E(CDIH)=2206.122 E(NOE )=9355.607 E(PLAN)=320.819 | ------------------------------------------------------------------------------- NBONDS: found 12362 intra-atom interactions --------------- cycle= 250 ------ stepsize= 0.0001 ----------------------- | Etotal =19218.460 grad(E)=22.018 E(BOND)=668.928 E(ANGL)=6007.462 | | E(VDW )=864.032 E(CDIH)=2193.552 E(NOE )=9159.252 E(PLAN)=325.235 | ------------------------------------------------------------------------------- --------------- cycle= 260 ------ stepsize= 0.0001 ----------------------- | Etotal =18963.741 grad(E)=19.958 E(BOND)=651.281 E(ANGL)=5990.797 | | E(VDW )=863.800 E(CDIH)=2163.335 E(NOE )=8970.424 E(PLAN)=324.103 | ------------------------------------------------------------------------------- NBONDS: found 12289 intra-atom interactions --------------- cycle= 270 ------ stepsize= 0.0001 ----------------------- | Etotal =18764.940 grad(E)=18.943 E(BOND)=624.589 E(ANGL)=5930.540 | | E(VDW )=863.752 E(CDIH)=2145.582 E(NOE )=8880.642 E(PLAN)=319.836 | ------------------------------------------------------------------------------- --------------- cycle= 280 ------ stepsize= 0.0001 ----------------------- | Etotal =18582.475 grad(E)=19.247 E(BOND)=619.317 E(ANGL)=5903.649 | | E(VDW )=855.708 E(CDIH)=2127.481 E(NOE )=8755.700 E(PLAN)=320.620 | ------------------------------------------------------------------------------- NBONDS: found 12217 intra-atom interactions --------------- cycle= 290 ------ stepsize= 0.0001 ----------------------- | Etotal =18403.178 grad(E)=17.392 E(BOND)=618.758 E(ANGL)=5850.717 | | E(VDW )=826.900 E(CDIH)=2106.056 E(NOE )=8693.022 E(PLAN)=307.725 | ------------------------------------------------------------------------------- --------------- cycle= 300 ------ stepsize= 0.0001 ----------------------- | Etotal =18223.673 grad(E)=19.191 E(BOND)=609.547 E(ANGL)=5767.660 | | E(VDW )=807.098 E(CDIH)=2101.471 E(NOE )=8644.956 E(PLAN)=292.940 | ------------------------------------------------------------------------------- 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= 0.192521295E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 0.00000 -0.00002 -0.00001 velocity [A/ps] : 0.15964 0.05868 0.02421 ang. mom. [amu A/ps] : -75792.56873-119122.59885 49070.61141 kin. ener. [Kcal/mol] : 2.38778 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00000 -0.00002 -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 12182 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=24537.897 E(kin)=6122.988 temperature=3034.198 | | Etotal =18414.909 grad(E)=72.059 E(BOND)=60.955 E(ANGL)=576.766 | | E(DIHE)=0.000 E(IMPR)=5930.723 E(VDW )=807.098 E(CDIH)=2101.471 | | E(NOE )=8644.956 E(PLAN)=292.940 | ------------------------------------------------------------------------------- NBONDS: found 12138 intra-atom interactions NBONDS: found 12053 intra-atom interactions NBONDS: found 12040 intra-atom interactions NBONDS: found 12025 intra-atom interactions NBONDS: found 11963 intra-atom interactions NBONDS: found 11905 intra-atom interactions NBONDS: found 11857 intra-atom interactions NBONDS: found 11819 intra-atom interactions NBONDS: found 11796 intra-atom interactions NBONDS: found 11809 intra-atom interactions NBONDS: found 11812 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=23547.832 E(kin)=6474.420 temperature=3208.347 | | Etotal =17073.412 grad(E)=68.132 E(BOND)=2199.830 E(ANGL)=4526.913 | | E(DIHE)=0.000 E(IMPR)=2688.369 E(VDW )=664.358 E(CDIH)=1267.827 | | E(NOE )=5538.641 E(PLAN)=187.474 | ------------------------------------------------------------------------------- NBONDS: found 11791 intra-atom interactions NBONDS: found 11747 intra-atom interactions NBONDS: found 11692 intra-atom interactions NBONDS: found 11650 intra-atom interactions NBONDS: found 11622 intra-atom interactions NBONDS: found 11594 intra-atom interactions NBONDS: found 11583 intra-atom interactions NBONDS: found 11562 intra-atom interactions NBONDS: found 11503 intra-atom interactions NBONDS: found 11434 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=21138.034 E(kin)=6940.049 temperature=3439.086 | | Etotal =14197.985 grad(E)=67.667 E(BOND)=2038.708 E(ANGL)=3789.628 | | E(DIHE)=0.000 E(IMPR)=2343.257 E(VDW )=404.150 E(CDIH)=1062.477 | | E(NOE )=4376.828 E(PLAN)=182.936 | ------------------------------------------------------------------------------- NBONDS: found 11340 intra-atom interactions NBONDS: found 11238 intra-atom interactions NBONDS: found 11157 intra-atom interactions NBONDS: found 11109 intra-atom interactions NBONDS: found 11045 intra-atom interactions NBONDS: found 10951 intra-atom interactions NBONDS: found 10871 intra-atom interactions NBONDS: found 10824 intra-atom interactions NBONDS: found 10798 intra-atom interactions NBONDS: found 10685 intra-atom interactions NBONDS: found 10625 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=18763.869 E(kin)=6437.863 temperature=3190.231 | | Etotal =12326.006 grad(E)=62.572 E(BOND)=1971.565 E(ANGL)=3429.173 | | E(DIHE)=0.000 E(IMPR)=1510.691 E(VDW )=438.806 E(CDIH)=717.146 | | E(NOE )=4078.492 E(PLAN)=180.132 | ------------------------------------------------------------------------------- NBONDS: found 10591 intra-atom interactions NBONDS: found 10550 intra-atom interactions NBONDS: found 10540 intra-atom interactions NBONDS: found 10511 intra-atom interactions NBONDS: found 10512 intra-atom interactions NBONDS: found 10500 intra-atom interactions NBONDS: found 10465 intra-atom interactions NBONDS: found 10472 intra-atom interactions NBONDS: found 10458 intra-atom interactions NBONDS: found 10463 intra-atom interactions NBONDS: found 10465 intra-atom interactions NBONDS: found 10424 intra-atom interactions NBONDS: found 10446 intra-atom interactions NBONDS: found 10431 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=15555.402 E(kin)=6397.567 temperature=3170.263 | | Etotal =9157.835 grad(E)=62.961 E(BOND)=2032.927 E(ANGL)=2743.777 | | E(DIHE)=0.000 E(IMPR)=916.618 E(VDW )=220.073 E(CDIH)=477.757 | | E(NOE )=2643.612 E(PLAN)=123.070 | ------------------------------------------------------------------------------- NBONDS: found 10439 intra-atom interactions NBONDS: found 10487 intra-atom interactions NBONDS: found 10545 intra-atom interactions NBONDS: found 10577 intra-atom interactions NBONDS: found 10582 intra-atom interactions NBONDS: found 10577 intra-atom interactions NBONDS: found 10536 intra-atom interactions NBONDS: found 10540 intra-atom interactions NBONDS: found 10576 intra-atom interactions NBONDS: found 10606 intra-atom interactions NBONDS: found 10596 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=14216.795 E(kin)=6113.081 temperature=3029.289 | | Etotal =8103.713 grad(E)=60.701 E(BOND)=1708.512 E(ANGL)=2378.281 | | E(DIHE)=0.000 E(IMPR)=921.484 E(VDW )=328.959 E(CDIH)=271.129 | | E(NOE )=2357.628 E(PLAN)=137.720 | ------------------------------------------------------------------------------- NBONDS: found 10580 intra-atom interactions NBONDS: found 10611 intra-atom interactions NBONDS: found 10566 intra-atom interactions NBONDS: found 10572 intra-atom interactions NBONDS: found 10528 intra-atom interactions NBONDS: found 10531 intra-atom interactions NBONDS: found 10519 intra-atom interactions NBONDS: found 10513 intra-atom interactions NBONDS: found 10458 intra-atom interactions NBONDS: found 10438 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=14215.218 E(kin)=6066.424 temperature=3006.168 | | Etotal =8148.794 grad(E)=60.855 E(BOND)=1792.916 E(ANGL)=2628.931 | | E(DIHE)=0.000 E(IMPR)=999.108 E(VDW )=198.556 E(CDIH)=239.243 | | E(NOE )=2137.115 E(PLAN)=152.924 | ------------------------------------------------------------------------------- NBONDS: found 10418 intra-atom interactions NBONDS: found 10398 intra-atom interactions NBONDS: found 10385 intra-atom interactions NBONDS: found 10392 intra-atom interactions NBONDS: found 10427 intra-atom interactions NBONDS: found 10432 intra-atom interactions NBONDS: found 10440 intra-atom interactions NBONDS: found 10416 intra-atom interactions NBONDS: found 10379 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=14195.985 E(kin)=6056.878 temperature=3001.437 | | Etotal =8139.107 grad(E)=61.519 E(BOND)=1867.657 E(ANGL)=2788.286 | | E(DIHE)=0.000 E(IMPR)=937.258 E(VDW )=235.326 E(CDIH)=215.859 | | E(NOE )=1988.771 E(PLAN)=105.950 | ------------------------------------------------------------------------------- NBONDS: found 10329 intra-atom interactions NBONDS: found 10298 intra-atom interactions NBONDS: found 10245 intra-atom interactions NBONDS: found 10241 intra-atom interactions NBONDS: found 10223 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00000 -0.00002 -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 -0.00002 -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 -0.00002 -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 10223 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=19182.982 E(kin)=6282.168 temperature=3113.078 | | Etotal =12900.814 grad(E)=112.429 E(BOND)=3469.686 E(ANGL)=4922.261 | | E(DIHE)=0.000 E(IMPR)=1961.286 E(VDW )=180.903 E(CDIH)=224.675 | | E(NOE )=2052.739 E(PLAN)=89.265 | ------------------------------------------------------------------------------- NBONDS: found 10258 intra-atom interactions NBONDS: found 10259 intra-atom interactions NBONDS: found 10192 intra-atom interactions NBONDS: found 10201 intra-atom interactions NBONDS: found 10251 intra-atom interactions NBONDS: found 10265 intra-atom interactions NBONDS: found 10281 intra-atom interactions NBONDS: found 10256 intra-atom interactions NBONDS: found 10293 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=16031.357 E(kin)=6293.992 temperature=3118.937 | | Etotal =9737.365 grad(E)=88.040 E(BOND)=1897.274 E(ANGL)=3486.790 | | E(DIHE)=0.000 E(IMPR)=1220.071 E(VDW )=349.735 E(CDIH)=347.627 | | E(NOE )=2358.810 E(PLAN)=77.058 | ------------------------------------------------------------------------------- NBONDS: found 10279 intra-atom interactions NBONDS: found 10263 intra-atom interactions NBONDS: found 10234 intra-atom interactions NBONDS: found 10215 intra-atom interactions NBONDS: found 10188 intra-atom interactions NBONDS: found 10170 intra-atom interactions NBONDS: found 10179 intra-atom interactions NBONDS: found 10167 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=15373.569 E(kin)=5985.355 temperature=2965.995 | | Etotal =9388.214 grad(E)=87.257 E(BOND)=2001.966 E(ANGL)=3354.691 | | E(DIHE)=0.000 E(IMPR)=985.092 E(VDW )=210.227 E(CDIH)=420.969 | | E(NOE )=2371.802 E(PLAN)=43.466 | ------------------------------------------------------------------------------- NBONDS: found 10179 intra-atom interactions NBONDS: found 10236 intra-atom interactions NBONDS: found 10241 intra-atom interactions NBONDS: found 10230 intra-atom interactions NBONDS: found 10300 intra-atom interactions NBONDS: found 10339 intra-atom interactions NBONDS: found 10337 intra-atom interactions NBONDS: found 10293 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=15068.513 E(kin)=6134.292 temperature=3039.799 | | Etotal =8934.221 grad(E)=86.355 E(BOND)=1967.715 E(ANGL)=2997.987 | | E(DIHE)=0.000 E(IMPR)=1008.918 E(VDW )=232.292 E(CDIH)=426.719 | | E(NOE )=2253.370 E(PLAN)=47.219 | ------------------------------------------------------------------------------- NBONDS: found 10260 intra-atom interactions NBONDS: found 10232 intra-atom interactions NBONDS: found 10186 intra-atom interactions NBONDS: found 10160 intra-atom interactions NBONDS: found 10207 intra-atom interactions NBONDS: found 10245 intra-atom interactions NBONDS: found 10299 intra-atom interactions NBONDS: found 10260 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=15038.571 E(kin)=5990.170 temperature=2968.381 | | Etotal =9048.401 grad(E)=88.187 E(BOND)=2077.011 E(ANGL)=2765.983 | | E(DIHE)=0.000 E(IMPR)=967.431 E(VDW )=308.143 E(CDIH)=347.463 | | E(NOE )=2479.183 E(PLAN)=103.186 | ------------------------------------------------------------------------------- NBONDS: found 10209 intra-atom interactions NBONDS: found 10214 intra-atom interactions NBONDS: found 10219 intra-atom interactions NBONDS: found 10228 intra-atom interactions NBONDS: found 10280 intra-atom interactions NBONDS: found 10249 intra-atom interactions NBONDS: found 10247 intra-atom interactions NBONDS: found 10273 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=15120.063 E(kin)=5997.741 temperature=2972.133 | | Etotal =9122.322 grad(E)=87.152 E(BOND)=1974.818 E(ANGL)=3117.216 | | E(DIHE)=0.000 E(IMPR)=1066.084 E(VDW )=314.817 E(CDIH)=287.239 | | E(NOE )=2328.566 E(PLAN)=33.582 | ------------------------------------------------------------------------------- NBONDS: found 10310 intra-atom interactions NBONDS: found 10303 intra-atom interactions NBONDS: found 10296 intra-atom interactions NBONDS: found 10346 intra-atom interactions NBONDS: found 10317 intra-atom interactions NBONDS: found 10348 intra-atom interactions NBONDS: found 10401 intra-atom interactions NBONDS: found 10419 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=15192.250 E(kin)=6218.570 temperature=3081.563 | | Etotal =8973.680 grad(E)=85.416 E(BOND)=1861.103 E(ANGL)=3100.563 | | E(DIHE)=0.000 E(IMPR)=1089.397 E(VDW )=239.344 E(CDIH)=278.717 | | E(NOE )=2351.959 E(PLAN)=52.596 | ------------------------------------------------------------------------------- NBONDS: found 10438 intra-atom interactions NBONDS: found 10464 intra-atom interactions NBONDS: found 10474 intra-atom interactions NBONDS: found 10443 intra-atom interactions NBONDS: found 10432 intra-atom interactions NBONDS: found 10393 intra-atom interactions NBONDS: found 10369 intra-atom interactions NBONDS: found 10356 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=15067.478 E(kin)=5980.556 temperature=2963.616 | | Etotal =9086.922 grad(E)=89.370 E(BOND)=2158.991 E(ANGL)=2933.431 | | E(DIHE)=0.000 E(IMPR)=944.139 E(VDW )=327.615 E(CDIH)=271.879 | | E(NOE )=2384.774 E(PLAN)=66.093 | ------------------------------------------------------------------------------- NBONDS: found 10413 intra-atom interactions NBONDS: found 10487 intra-atom interactions NBONDS: found 10447 intra-atom interactions NBONDS: found 10467 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00000 -0.00002 -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 -0.00002 -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 -0.00002 -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 10468 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=16126.075 E(kin)=6032.181 temperature=2989.199 | | Etotal =10093.894 grad(E)=101.254 E(BOND)=1943.743 E(ANGL)=2953.165 | | E(DIHE)=0.000 E(IMPR)=2103.844 E(VDW )=292.322 E(CDIH)=289.697 | | E(NOE )=2472.559 E(PLAN)=38.564 | ------------------------------------------------------------------------------- NBONDS: found 10444 intra-atom interactions NBONDS: found 10450 intra-atom interactions NBONDS: found 10516 intra-atom interactions NBONDS: found 10591 intra-atom interactions NBONDS: found 10597 intra-atom interactions NBONDS: found 10672 intra-atom interactions NBONDS: found 10672 intra-atom interactions NBONDS: found 10737 intra-atom interactions NBONDS: found 10821 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=14936.754 E(kin)=6236.311 temperature=3090.354 | | Etotal =8700.443 grad(E)=92.783 E(BOND)=1946.218 E(ANGL)=2944.782 | | E(DIHE)=0.000 E(IMPR)=817.743 E(VDW )=347.055 E(CDIH)=379.492 | | E(NOE )=2213.264 E(PLAN)=51.888 | ------------------------------------------------------------------------------- NBONDS: found 10883 intra-atom interactions NBONDS: found 10981 intra-atom interactions NBONDS: found 11062 intra-atom interactions NBONDS: found 11158 intra-atom interactions NBONDS: found 11218 intra-atom interactions NBONDS: found 11237 intra-atom interactions NBONDS: found 11245 intra-atom interactions NBONDS: found 11230 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=14106.017 E(kin)=6238.286 temperature=3091.333 | | Etotal =7867.730 grad(E)=90.194 E(BOND)=1807.993 E(ANGL)=2558.336 | | E(DIHE)=0.000 E(IMPR)=872.984 E(VDW )=363.446 E(CDIH)=336.027 | | E(NOE )=1868.336 E(PLAN)=60.610 | ------------------------------------------------------------------------------- NBONDS: found 11249 intra-atom interactions NBONDS: found 11215 intra-atom interactions NBONDS: found 11184 intra-atom interactions NBONDS: found 11220 intra-atom interactions NBONDS: found 11287 intra-atom interactions NBONDS: found 11330 intra-atom interactions NBONDS: found 11429 intra-atom interactions NBONDS: found 11457 intra-atom interactions NBONDS: found 11499 intra-atom interactions NBONDS: found 11506 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=13808.393 E(kin)=5873.889 temperature=2910.759 | | Etotal =7934.504 grad(E)=91.523 E(BOND)=2010.549 E(ANGL)=2464.080 | | E(DIHE)=0.000 E(IMPR)=857.238 E(VDW )=388.185 E(CDIH)=320.459 | | E(NOE )=1836.110 E(PLAN)=57.883 | ------------------------------------------------------------------------------- NBONDS: found 11537 intra-atom interactions NBONDS: found 11556 intra-atom interactions NBONDS: found 11581 intra-atom interactions NBONDS: found 11590 intra-atom interactions NBONDS: found 11655 intra-atom interactions NBONDS: found 11681 intra-atom interactions NBONDS: found 11740 intra-atom interactions NBONDS: found 11799 intra-atom interactions NBONDS: found 11855 intra-atom interactions NBONDS: found 11873 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=13976.400 E(kin)=6219.366 temperature=3081.957 | | Etotal =7757.034 grad(E)=86.109 E(BOND)=1742.537 E(ANGL)=2583.668 | | E(DIHE)=0.000 E(IMPR)=779.039 E(VDW )=406.850 E(CDIH)=326.551 | | E(NOE )=1864.741 E(PLAN)=53.647 | ------------------------------------------------------------------------------- NBONDS: found 11965 intra-atom interactions NBONDS: found 12007 intra-atom interactions NBONDS: found 12058 intra-atom interactions NBONDS: found 12082 intra-atom interactions NBONDS: found 12051 intra-atom interactions NBONDS: found 12013 intra-atom interactions NBONDS: found 11936 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=13987.158 E(kin)=6008.423 temperature=2977.426 | | Etotal =7978.734 grad(E)=90.502 E(BOND)=1912.872 E(ANGL)=2562.573 | | E(DIHE)=0.000 E(IMPR)=822.609 E(VDW )=397.270 E(CDIH)=304.572 | | E(NOE )=1910.434 E(PLAN)=68.404 | ------------------------------------------------------------------------------- NBONDS: found 11909 intra-atom interactions NBONDS: found 11921 intra-atom interactions NBONDS: found 11942 intra-atom interactions NBONDS: found 12004 intra-atom interactions NBONDS: found 12032 intra-atom interactions NBONDS: found 12054 intra-atom interactions NBONDS: found 12064 intra-atom interactions NBONDS: found 12060 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=13631.577 E(kin)=5887.644 temperature=2917.575 | | Etotal =7743.933 grad(E)=91.883 E(BOND)=1847.383 E(ANGL)=2469.656 | | E(DIHE)=0.000 E(IMPR)=909.137 E(VDW )=403.203 E(CDIH)=324.042 | | E(NOE )=1727.775 E(PLAN)=62.737 | ------------------------------------------------------------------------------- NBONDS: found 12028 intra-atom interactions NBONDS: found 12038 intra-atom interactions NBONDS: found 11966 intra-atom interactions NBONDS: found 11895 intra-atom interactions NBONDS: found 11902 intra-atom interactions NBONDS: found 11886 intra-atom interactions NBONDS: found 11870 intra-atom interactions NBONDS: found 11891 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=13680.060 E(kin)=6082.626 temperature=3014.196 | | Etotal =7597.434 grad(E)=89.121 E(BOND)=1830.132 E(ANGL)=2418.482 | | E(DIHE)=0.000 E(IMPR)=716.702 E(VDW )=395.948 E(CDIH)=337.432 | | E(NOE )=1835.928 E(PLAN)=62.812 | ------------------------------------------------------------------------------- NBONDS: found 11973 intra-atom interactions NBONDS: found 12059 intra-atom interactions NBONDS: found 12107 intra-atom interactions NBONDS: found 12052 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00000 -0.00002 -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 -0.00002 -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 -0.00002 -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 10734 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=18689.659 E(kin)=5893.430 temperature=2920.442 | | Etotal =12796.228 grad(E)=179.596 E(BOND)=3793.579 E(ANGL)=4930.698 | | E(DIHE)=0.000 E(IMPR)=1534.194 E(VDW )=69.922 E(CDIH)=344.272 | | E(NOE )=2051.388 E(PLAN)=72.175 | ------------------------------------------------------------------------------- NBONDS: found 10844 intra-atom interactions NBONDS: found 10863 intra-atom interactions NBONDS: found 10894 intra-atom interactions NBONDS: found 10882 intra-atom interactions NBONDS: found 10871 intra-atom interactions NBONDS: found 10874 intra-atom interactions NBONDS: found 10875 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=14669.675 E(kin)=6148.482 temperature=3046.831 | | Etotal =8521.193 grad(E)=136.616 E(BOND)=2197.114 E(ANGL)=2891.492 | | E(DIHE)=0.000 E(IMPR)=918.565 E(VDW )=74.215 E(CDIH)=353.327 | | E(NOE )=2021.546 E(PLAN)=64.935 | ------------------------------------------------------------------------------- NBONDS: found 10824 intra-atom interactions NBONDS: found 10782 intra-atom interactions NBONDS: found 10824 intra-atom interactions NBONDS: found 10810 intra-atom interactions NBONDS: found 10764 intra-atom interactions NBONDS: found 10764 intra-atom interactions NBONDS: found 10731 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=14073.109 E(kin)=5883.436 temperature=2915.489 | | Etotal =8189.673 grad(E)=136.982 E(BOND)=2111.030 E(ANGL)=2779.345 | | E(DIHE)=0.000 E(IMPR)=898.317 E(VDW )=74.902 E(CDIH)=344.602 | | E(NOE )=1921.924 E(PLAN)=59.552 | ------------------------------------------------------------------------------- NBONDS: found 10761 intra-atom interactions NBONDS: found 10748 intra-atom interactions NBONDS: found 10724 intra-atom interactions NBONDS: found 10706 intra-atom interactions NBONDS: found 10734 intra-atom interactions NBONDS: found 10712 intra-atom interactions NBONDS: found 10707 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=13866.666 E(kin)=5977.497 temperature=2962.101 | | Etotal =7889.169 grad(E)=128.172 E(BOND)=2068.530 E(ANGL)=2679.758 | | E(DIHE)=0.000 E(IMPR)=777.844 E(VDW )=74.820 E(CDIH)=346.630 | | E(NOE )=1874.034 E(PLAN)=67.553 | ------------------------------------------------------------------------------- NBONDS: found 10729 intra-atom interactions NBONDS: found 10786 intra-atom interactions NBONDS: found 10861 intra-atom interactions NBONDS: found 10894 intra-atom interactions NBONDS: found 10873 intra-atom interactions NBONDS: found 10952 intra-atom interactions NBONDS: found 10963 intra-atom interactions NBONDS: found 11001 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=13838.775 E(kin)=6376.624 temperature=3159.885 | | Etotal =7462.151 grad(E)=127.517 E(BOND)=1948.597 E(ANGL)=2550.185 | | E(DIHE)=0.000 E(IMPR)=736.520 E(VDW )=81.078 E(CDIH)=312.551 | | E(NOE )=1792.863 E(PLAN)=40.357 | ------------------------------------------------------------------------------- NBONDS: found 11090 intra-atom interactions NBONDS: found 11122 intra-atom interactions NBONDS: found 11091 intra-atom interactions NBONDS: found 11110 intra-atom interactions NBONDS: found 11154 intra-atom interactions NBONDS: found 11154 intra-atom interactions NBONDS: found 11206 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=13903.753 E(kin)=6009.245 temperature=2977.833 | | Etotal =7894.508 grad(E)=130.689 E(BOND)=2032.678 E(ANGL)=2818.283 | | E(DIHE)=0.000 E(IMPR)=786.666 E(VDW )=88.874 E(CDIH)=348.054 | | E(NOE )=1781.444 E(PLAN)=38.510 | ------------------------------------------------------------------------------- NBONDS: found 11285 intra-atom interactions NBONDS: found 11303 intra-atom interactions NBONDS: found 11313 intra-atom interactions NBONDS: found 11251 intra-atom interactions NBONDS: found 11212 intra-atom interactions NBONDS: found 11224 intra-atom interactions NBONDS: found 11276 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=13898.685 E(kin)=6227.996 temperature=3086.234 | | Etotal =7670.689 grad(E)=126.381 E(BOND)=2002.365 E(ANGL)=2532.160 | | E(DIHE)=0.000 E(IMPR)=813.201 E(VDW )=85.128 E(CDIH)=311.007 | | E(NOE )=1874.440 E(PLAN)=52.387 | ------------------------------------------------------------------------------- NBONDS: found 11289 intra-atom interactions NBONDS: found 11300 intra-atom interactions NBONDS: found 11247 intra-atom interactions NBONDS: found 11204 intra-atom interactions NBONDS: found 11203 intra-atom interactions NBONDS: found 11199 intra-atom interactions NBONDS: found 11205 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=13922.372 E(kin)=5940.689 temperature=2943.861 | | Etotal =7981.684 grad(E)=127.862 E(BOND)=1994.346 E(ANGL)=2750.329 | | E(DIHE)=0.000 E(IMPR)=810.388 E(VDW )=79.385 E(CDIH)=295.070 | | E(NOE )=2002.039 E(PLAN)=50.126 | ------------------------------------------------------------------------------- NBONDS: found 11152 intra-atom interactions NBONDS: found 11123 intra-atom interactions NBONDS: found 11008 intra-atom interactions NBONDS: found 11013 intra-atom interactions NBONDS: found 11045 intra-atom interactions NBONDS: found 11052 intra-atom interactions NBONDS: found 11058 intra-atom interactions --------------- step= 800 at 1.60000 ps -------------------------------- | E(kin)+E(total)=13952.839 E(kin)=6170.364 temperature=3057.675 | | Etotal =7782.474 grad(E)=131.302 E(BOND)=2051.194 E(ANGL)=2516.594 | | E(DIHE)=0.000 E(IMPR)=774.188 E(VDW )=78.045 E(CDIH)=283.139 | | E(NOE )=2018.129 E(PLAN)=61.186 | ------------------------------------------------------------------------------- NBONDS: found 11086 intra-atom interactions NBONDS: found 11106 intra-atom interactions NBONDS: found 11213 intra-atom interactions NBONDS: found 11303 intra-atom interactions NBONDS: found 11375 intra-atom interactions NBONDS: found 11487 intra-atom interactions NBONDS: found 11607 intra-atom interactions --------------- step= 900 at 1.80000 ps -------------------------------- | E(kin)+E(total)=13864.385 E(kin)=6056.160 temperature=3001.082 | | Etotal =7808.225 grad(E)=129.550 E(BOND)=2091.898 E(ANGL)=2677.604 | | E(DIHE)=0.000 E(IMPR)=777.915 E(VDW )=89.744 E(CDIH)=319.652 | | E(NOE )=1794.685 E(PLAN)=56.726 | ------------------------------------------------------------------------------- NBONDS: found 11691 intra-atom interactions NBONDS: found 11674 intra-atom interactions NBONDS: found 11664 intra-atom interactions NBONDS: found 11696 intra-atom interactions NBONDS: found 11717 intra-atom interactions NBONDS: found 11796 intra-atom interactions NBONDS: found 11841 intra-atom interactions --------------- step= 1000 at 2.00000 ps -------------------------------- | E(kin)+E(total)=13843.288 E(kin)=6308.805 temperature=3126.278 | | Etotal =7534.483 grad(E)=128.768 E(BOND)=1904.150 E(ANGL)=2547.047 | | E(DIHE)=0.000 E(IMPR)=806.349 E(VDW )=99.162 E(CDIH)=263.324 | | E(NOE )=1871.757 E(PLAN)=42.694 | ------------------------------------------------------------------------------- NBONDS: found 11782 intra-atom interactions NBONDS: found 11770 intra-atom interactions NBONDS: found 11736 intra-atom interactions NBONDS: found 11678 intra-atom interactions NBONDS: found 11613 intra-atom interactions NBONDS: found 11595 intra-atom interactions NBONDS: found 11529 intra-atom interactions --------------- step= 1100 at 2.20000 ps -------------------------------- | E(kin)+E(total)=13928.659 E(kin)=6001.672 temperature=2974.080 | | Etotal =7926.986 grad(E)=129.010 E(BOND)=1988.842 E(ANGL)=2825.552 | | E(DIHE)=0.000 E(IMPR)=786.396 E(VDW )=95.748 E(CDIH)=276.638 | | E(NOE )=1907.471 E(PLAN)=46.339 | ------------------------------------------------------------------------------- NBONDS: found 11398 intra-atom interactions NBONDS: found 11362 intra-atom interactions NBONDS: found 11365 intra-atom interactions NBONDS: found 11341 intra-atom interactions NBONDS: found 11292 intra-atom interactions NBONDS: found 11282 intra-atom interactions NBONDS: found 11274 intra-atom interactions --------------- step= 1200 at 2.40000 ps -------------------------------- | E(kin)+E(total)=13785.470 E(kin)=6060.485 temperature=3003.225 | | Etotal =7724.985 grad(E)=128.900 E(BOND)=1940.740 E(ANGL)=2610.462 | | E(DIHE)=0.000 E(IMPR)=756.755 E(VDW )=86.018 E(CDIH)=355.895 | | E(NOE )=1928.794 E(PLAN)=46.322 | ------------------------------------------------------------------------------- NBONDS: found 11232 intra-atom interactions NBONDS: found 11208 intra-atom interactions NBONDS: found 11210 intra-atom interactions NBONDS: found 11228 intra-atom interactions NBONDS: found 11217 intra-atom interactions NBONDS: found 11239 intra-atom interactions NBONDS: found 11300 intra-atom interactions NBONDS: found 11199 intra-atom interactions --------------- step= 1300 at 2.60000 ps -------------------------------- | E(kin)+E(total)=13904.044 E(kin)=6129.277 temperature=3037.314 | | Etotal =7774.767 grad(E)=127.988 E(BOND)=2028.725 E(ANGL)=2532.869 | | E(DIHE)=0.000 E(IMPR)=798.096 E(VDW )=78.445 E(CDIH)=306.793 | | E(NOE )=1957.926 E(PLAN)=71.913 | ------------------------------------------------------------------------------- NBONDS: found 11109 intra-atom interactions NBONDS: found 11065 intra-atom interactions NBONDS: found 11036 intra-atom interactions NBONDS: found 11032 intra-atom interactions NBONDS: found 11003 intra-atom interactions NBONDS: found 11001 intra-atom interactions NBONDS: found 10943 intra-atom interactions --------------- step= 1400 at 2.80000 ps -------------------------------- | E(kin)+E(total)=13845.123 E(kin)=6108.787 temperature=3027.161 | | Etotal =7736.336 grad(E)=131.517 E(BOND)=1988.233 E(ANGL)=2610.011 | | E(DIHE)=0.000 E(IMPR)=790.449 E(VDW )=78.043 E(CDIH)=269.965 | | E(NOE )=1947.777 E(PLAN)=51.857 | ------------------------------------------------------------------------------- NBONDS: found 10845 intra-atom interactions NBONDS: found 10815 intra-atom interactions NBONDS: found 10824 intra-atom interactions NBONDS: found 10800 intra-atom interactions NBONDS: found 10758 intra-atom interactions NBONDS: found 10715 intra-atom interactions NBONDS: found 10703 intra-atom interactions NBONDS: found 10806 intra-atom interactions --------------- step= 1500 at 3.00000 ps -------------------------------- | E(kin)+E(total)=13777.573 E(kin)=6032.035 temperature=2989.127 | | Etotal =7745.538 grad(E)=127.405 E(BOND)=1911.863 E(ANGL)=2724.633 | | E(DIHE)=0.000 E(IMPR)=784.509 E(VDW )=73.079 E(CDIH)=304.978 | | E(NOE )=1885.331 E(PLAN)=61.144 | ------------------------------------------------------------------------------- NBONDS: found 10786 intra-atom interactions NBONDS: found 10746 intra-atom interactions NBONDS: found 10687 intra-atom interactions NBONDS: found 10685 intra-atom interactions NBONDS: found 10653 intra-atom interactions NBONDS: found 10595 intra-atom interactions NBONDS: found 10595 intra-atom interactions --------------- step= 1600 at 3.20000 ps -------------------------------- | E(kin)+E(total)=13895.865 E(kin)=6068.672 temperature=3007.282 | | Etotal =7827.192 grad(E)=130.350 E(BOND)=2084.674 E(ANGL)=2740.648 | | E(DIHE)=0.000 E(IMPR)=711.744 E(VDW )=72.400 E(CDIH)=310.587 | | E(NOE )=1848.246 E(PLAN)=58.894 | ------------------------------------------------------------------------------- NBONDS: found 10595 intra-atom interactions NBONDS: found 10568 intra-atom interactions NBONDS: found 10602 intra-atom interactions NBONDS: found 10553 intra-atom interactions NBONDS: found 10605 intra-atom interactions NBONDS: found 10594 intra-atom interactions NBONDS: found 10497 intra-atom interactions --------------- step= 1700 at 3.40000 ps -------------------------------- | E(kin)+E(total)=13874.438 E(kin)=5902.939 temperature=2925.154 | | Etotal =7971.499 grad(E)=128.877 E(BOND)=2230.862 E(ANGL)=2559.879 | | E(DIHE)=0.000 E(IMPR)=771.775 E(VDW )=66.837 E(CDIH)=310.486 | | E(NOE )=1995.300 E(PLAN)=36.361 | ------------------------------------------------------------------------------- NBONDS: found 10535 intra-atom interactions NBONDS: found 10540 intra-atom interactions NBONDS: found 10556 intra-atom interactions NBONDS: found 10468 intra-atom interactions NBONDS: found 10395 intra-atom interactions NBONDS: found 10300 intra-atom interactions NBONDS: found 10312 intra-atom interactions --------------- step= 1800 at 3.60000 ps -------------------------------- | E(kin)+E(total)=13907.772 E(kin)=6073.665 temperature=3009.756 | | Etotal =7834.107 grad(E)=127.212 E(BOND)=2008.899 E(ANGL)=2752.408 | | E(DIHE)=0.000 E(IMPR)=750.578 E(VDW )=63.424 E(CDIH)=290.618 | | E(NOE )=1904.873 E(PLAN)=63.307 | ------------------------------------------------------------------------------- NBONDS: found 10347 intra-atom interactions NBONDS: found 10344 intra-atom interactions NBONDS: found 10348 intra-atom interactions NBONDS: found 10269 intra-atom interactions NBONDS: found 10279 intra-atom interactions NBONDS: found 10235 intra-atom interactions NBONDS: found 10263 intra-atom interactions NBONDS: found 10309 intra-atom interactions --------------- step= 1900 at 3.80000 ps -------------------------------- | E(kin)+E(total)=13889.301 E(kin)=6309.699 temperature=3126.721 | | Etotal =7579.602 grad(E)=128.061 E(BOND)=2101.332 E(ANGL)=2532.127 | | E(DIHE)=0.000 E(IMPR)=654.352 E(VDW )=71.635 E(CDIH)=316.517 | | E(NOE )=1862.544 E(PLAN)=41.096 | ------------------------------------------------------------------------------- NBONDS: found 10234 intra-atom interactions NBONDS: found 10288 intra-atom interactions NBONDS: found 10293 intra-atom interactions NBONDS: found 10278 intra-atom interactions NBONDS: found 10265 intra-atom interactions NBONDS: found 10331 intra-atom interactions NBONDS: found 10329 intra-atom interactions --------------- step= 2000 at 4.00000 ps -------------------------------- | E(kin)+E(total)=13959.516 E(kin)=6048.798 temperature=2997.433 | | Etotal =7910.718 grad(E)=130.226 E(BOND)=2030.749 E(ANGL)=2693.817 | | E(DIHE)=0.000 E(IMPR)=719.227 E(VDW )=74.795 E(CDIH)=352.795 | | E(NOE )=2009.351 E(PLAN)=29.985 | ------------------------------------------------------------------------------- NBONDS: found 10339 intra-atom interactions NBONDS: found 10298 intra-atom interactions NBONDS: found 10199 intra-atom interactions NBONDS: found 10196 intra-atom interactions NBONDS: found 10161 intra-atom interactions NBONDS: found 10140 intra-atom interactions NBONDS: found 10069 intra-atom interactions --------------- step= 2100 at 4.20000 ps -------------------------------- | E(kin)+E(total)=13888.318 E(kin)=6136.156 temperature=3040.723 | | Etotal =7752.162 grad(E)=124.287 E(BOND)=1865.148 E(ANGL)=2877.718 | | E(DIHE)=0.000 E(IMPR)=800.530 E(VDW )=70.450 E(CDIH)=258.260 | | E(NOE )=1847.660 E(PLAN)=32.396 | ------------------------------------------------------------------------------- NBONDS: found 10091 intra-atom interactions NBONDS: found 10099 intra-atom interactions NBONDS: found 10082 intra-atom interactions NBONDS: found 10085 intra-atom interactions NBONDS: found 10095 intra-atom interactions NBONDS: found 10089 intra-atom interactions NBONDS: found 10053 intra-atom interactions --------------- step= 2200 at 4.40000 ps -------------------------------- | E(kin)+E(total)=13764.285 E(kin)=6124.250 temperature=3034.823 | | Etotal =7640.035 grad(E)=127.547 E(BOND)=1894.848 E(ANGL)=2710.343 | | E(DIHE)=0.000 E(IMPR)=734.368 E(VDW )=66.085 E(CDIH)=251.164 | | E(NOE )=1927.395 E(PLAN)=55.832 | ------------------------------------------------------------------------------- NBONDS: found 10045 intra-atom interactions NBONDS: found 10044 intra-atom interactions NBONDS: found 10031 intra-atom interactions NBONDS: found 10088 intra-atom interactions NBONDS: found 10092 intra-atom interactions NBONDS: found 10043 intra-atom interactions NBONDS: found 10013 intra-atom interactions NBONDS: found 10037 intra-atom interactions --------------- step= 2300 at 4.60000 ps -------------------------------- | E(kin)+E(total)=13813.363 E(kin)=5842.515 temperature=2895.212 | | Etotal =7970.847 grad(E)=130.199 E(BOND)=1979.731 E(ANGL)=2963.126 | | E(DIHE)=0.000 E(IMPR)=824.898 E(VDW )=67.520 E(CDIH)=327.733 | | E(NOE )=1763.728 E(PLAN)=44.111 | ------------------------------------------------------------------------------- NBONDS: found 9978 intra-atom interactions NBONDS: found 10046 intra-atom interactions NBONDS: found 10050 intra-atom interactions NBONDS: found 10025 intra-atom interactions NBONDS: found 10067 intra-atom interactions NBONDS: found 10047 intra-atom interactions NBONDS: found 10025 intra-atom interactions --------------- step= 2400 at 4.80000 ps -------------------------------- | E(kin)+E(total)=13887.998 E(kin)=5938.055 temperature=2942.555 | | Etotal =7949.943 grad(E)=128.903 E(BOND)=2020.996 E(ANGL)=2917.811 | | E(DIHE)=0.000 E(IMPR)=833.456 E(VDW )=63.210 E(CDIH)=249.469 | | E(NOE )=1828.314 E(PLAN)=36.688 | ------------------------------------------------------------------------------- NBONDS: found 9981 intra-atom interactions NBONDS: found 9967 intra-atom interactions NBONDS: found 9951 intra-atom interactions NBONDS: found 9912 intra-atom interactions NBONDS: found 9868 intra-atom interactions NBONDS: found 9840 intra-atom interactions NBONDS: found 9827 intra-atom interactions --------------- step= 2500 at 5.00000 ps -------------------------------- | E(kin)+E(total)=13742.243 E(kin)=6295.052 temperature=3119.463 | | Etotal =7447.190 grad(E)=121.513 E(BOND)=2022.950 E(ANGL)=2489.350 | | E(DIHE)=0.000 E(IMPR)=739.703 E(VDW )=57.608 E(CDIH)=240.754 | | E(NOE )=1820.606 E(PLAN)=76.220 | ------------------------------------------------------------------------------- NBONDS: found 9714 intra-atom interactions NBONDS: found 9681 intra-atom interactions NBONDS: found 9678 intra-atom interactions NBONDS: found 9715 intra-atom interactions NBONDS: found 9765 intra-atom interactions NBONDS: found 9756 intra-atom interactions NBONDS: found 9673 intra-atom interactions --------------- step= 2600 at 5.20000 ps -------------------------------- | E(kin)+E(total)=13829.279 E(kin)=6114.575 temperature=3030.029 | | Etotal =7714.703 grad(E)=126.788 E(BOND)=1955.248 E(ANGL)=2648.146 | | E(DIHE)=0.000 E(IMPR)=804.145 E(VDW )=58.239 E(CDIH)=254.122 | | E(NOE )=1913.347 E(PLAN)=81.457 | ------------------------------------------------------------------------------- NBONDS: found 9759 intra-atom interactions NBONDS: found 9807 intra-atom interactions NBONDS: found 9770 intra-atom interactions NBONDS: found 9768 intra-atom interactions NBONDS: found 9724 intra-atom interactions NBONDS: found 9738 intra-atom interactions NBONDS: found 9712 intra-atom interactions --------------- step= 2700 at 5.40000 ps -------------------------------- | E(kin)+E(total)=13815.428 E(kin)=6171.036 temperature=3058.007 | | Etotal =7644.393 grad(E)=129.239 E(BOND)=1780.091 E(ANGL)=2786.340 | | E(DIHE)=0.000 E(IMPR)=925.846 E(VDW )=56.886 E(CDIH)=283.590 | | E(NOE )=1767.202 E(PLAN)=44.437 | ------------------------------------------------------------------------------- NBONDS: found 9716 intra-atom interactions NBONDS: found 9751 intra-atom interactions NBONDS: found 9717 intra-atom interactions NBONDS: found 9628 intra-atom interactions NBONDS: found 9628 intra-atom interactions NBONDS: found 9623 intra-atom interactions NBONDS: found 9568 intra-atom interactions --------------- step= 2800 at 5.60000 ps -------------------------------- | E(kin)+E(total)=13888.474 E(kin)=5799.391 temperature=2873.842 | | Etotal =8089.083 grad(E)=133.327 E(BOND)=2181.555 E(ANGL)=2642.601 | | E(DIHE)=0.000 E(IMPR)=823.765 E(VDW )=52.218 E(CDIH)=316.999 | | E(NOE )=2014.292 E(PLAN)=57.654 | ------------------------------------------------------------------------------- NBONDS: found 9570 intra-atom interactions NBONDS: found 9608 intra-atom interactions NBONDS: found 9623 intra-atom interactions NBONDS: found 9700 intra-atom interactions NBONDS: found 9721 intra-atom interactions NBONDS: found 9707 intra-atom interactions NBONDS: found 9752 intra-atom interactions --------------- step= 2900 at 5.80000 ps -------------------------------- | E(kin)+E(total)=13805.026 E(kin)=6129.549 temperature=3037.449 | | Etotal =7675.478 grad(E)=129.555 E(BOND)=2002.619 E(ANGL)=2646.866 | | E(DIHE)=0.000 E(IMPR)=744.019 E(VDW )=52.418 E(CDIH)=290.268 | | E(NOE )=1883.351 E(PLAN)=55.938 | ------------------------------------------------------------------------------- NBONDS: found 9774 intra-atom interactions NBONDS: found 9799 intra-atom interactions NBONDS: found 9824 intra-atom interactions NBONDS: found 9806 intra-atom interactions NBONDS: found 9905 intra-atom interactions NBONDS: found 9911 intra-atom interactions NBONDS: found 9897 intra-atom interactions --------------- step= 3000 at 6.00000 ps -------------------------------- | E(kin)+E(total)=13899.601 E(kin)=6085.588 temperature=3015.664 | | Etotal =7814.013 grad(E)=128.737 E(BOND)=1923.883 E(ANGL)=2784.708 | | E(DIHE)=0.000 E(IMPR)=813.055 E(VDW )=55.818 E(CDIH)=296.943 | | E(NOE )=1875.196 E(PLAN)=64.411 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 0.00000 -0.00002 -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 -0.00002 -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 -0.00002 -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 9919 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=22182.070 E(kin)=6085.588 temperature=3015.664 | | Etotal =16096.482 grad(E)=318.129 E(BOND)=4809.707 E(ANGL)=6961.770 | | E(DIHE)=0.000 E(IMPR)=2032.637 E(VDW )=55.818 E(CDIH)=296.943 | | E(NOE )=1875.196 E(PLAN)=64.411 | ------------------------------------------------------------------------------- NBONDS: found 9923 intra-atom interactions NBONDS: found 9881 intra-atom interactions NBONDS: found 9826 intra-atom interactions NBONDS: found 9814 intra-atom interactions NBONDS: found 9759 intra-atom interactions NBONDS: found 9644 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=15645.806 E(kin)=6503.499 temperature=3222.757 | | Etotal =9142.307 grad(E)=225.580 E(BOND)=2373.391 E(ANGL)=3275.587 | | E(DIHE)=0.000 E(IMPR)=1042.296 E(VDW )=51.693 E(CDIH)=278.742 | | E(NOE )=2078.094 E(PLAN)=42.505 | ------------------------------------------------------------------------------- NBONDS: found 9617 intra-atom interactions NBONDS: found 9577 intra-atom interactions NBONDS: found 9480 intra-atom interactions NBONDS: found 9464 intra-atom interactions NBONDS: found 9400 intra-atom interactions NBONDS: found 9365 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=14704.356 E(kin)=6258.559 temperature=3101.379 | | Etotal =8445.798 grad(E)=212.040 E(BOND)=2069.356 E(ANGL)=2861.459 | | E(DIHE)=0.000 E(IMPR)=938.130 E(VDW )=47.923 E(CDIH)=309.513 | | E(NOE )=2161.893 E(PLAN)=57.524 | ------------------------------------------------------------------------------- NBONDS: found 9369 intra-atom interactions NBONDS: found 9304 intra-atom interactions NBONDS: found 9337 intra-atom interactions NBONDS: found 9313 intra-atom interactions NBONDS: found 9311 intra-atom interactions NBONDS: found 9268 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=14574.817 E(kin)=6100.846 temperature=3023.225 | | Etotal =8473.971 grad(E)=215.767 E(BOND)=2119.863 E(ANGL)=2854.376 | | E(DIHE)=0.000 E(IMPR)=964.528 E(VDW )=43.777 E(CDIH)=340.453 | | E(NOE )=2114.656 E(PLAN)=36.318 | ------------------------------------------------------------------------------- NBONDS: found 9217 intra-atom interactions NBONDS: found 9184 intra-atom interactions NBONDS: found 9215 intra-atom interactions NBONDS: found 9162 intra-atom interactions NBONDS: found 9179 intra-atom interactions NBONDS: found 9196 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=14578.927 E(kin)=5820.266 temperature=2884.186 | | Etotal =8758.660 grad(E)=215.587 E(BOND)=2288.968 E(ANGL)=3046.767 | | E(DIHE)=0.000 E(IMPR)=825.643 E(VDW )=42.708 E(CDIH)=315.991 | | E(NOE )=2187.905 E(PLAN)=50.677 | ------------------------------------------------------------------------------- NBONDS: found 9201 intra-atom interactions NBONDS: found 9214 intra-atom interactions NBONDS: found 9190 intra-atom interactions NBONDS: found 9189 intra-atom interactions NBONDS: found 9205 intra-atom interactions NBONDS: found 9247 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=14584.980 E(kin)=6171.888 temperature=3058.430 | | Etotal =8413.092 grad(E)=214.368 E(BOND)=2222.579 E(ANGL)=2828.203 | | E(DIHE)=0.000 E(IMPR)=882.636 E(VDW )=42.825 E(CDIH)=348.391 | | E(NOE )=2050.196 E(PLAN)=38.264 | ------------------------------------------------------------------------------- NBONDS: found 9271 intra-atom interactions NBONDS: found 9258 intra-atom interactions NBONDS: found 9249 intra-atom interactions NBONDS: found 9232 intra-atom interactions NBONDS: found 9280 intra-atom interactions NBONDS: found 9221 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=14579.858 E(kin)=6060.764 temperature=3003.363 | | Etotal =8519.094 grad(E)=212.210 E(BOND)=2243.060 E(ANGL)=2887.672 | | E(DIHE)=0.000 E(IMPR)=800.317 E(VDW )=42.369 E(CDIH)=274.773 | | E(NOE )=2214.326 E(PLAN)=56.577 | ------------------------------------------------------------------------------- NBONDS: found 9169 intra-atom interactions NBONDS: found 9239 intra-atom interactions NBONDS: found 9249 intra-atom interactions NBONDS: found 9222 intra-atom interactions NBONDS: found 9210 intra-atom interactions NBONDS: found 9205 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=14545.599 E(kin)=5826.510 temperature=2887.281 | | Etotal =8719.088 grad(E)=221.951 E(BOND)=2267.708 E(ANGL)=3121.889 | | E(DIHE)=0.000 E(IMPR)=875.864 E(VDW )=40.127 E(CDIH)=275.121 | | E(NOE )=2078.735 E(PLAN)=59.644 | ------------------------------------------------------------------------------- NBONDS: found 9274 intra-atom interactions NBONDS: found 9243 intra-atom interactions NBONDS: found 9281 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00000 -0.00002 -0.00001 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> if ($image=1) then NEXTCD: condition evaluated as true X-PLOR> vector do (store7=x) (all) ! Store first image in stores. SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store8=y) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store9=z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store4=vx) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store5=vy) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store6=vz) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> end if X-PLOR> X-PLOR>end loop imag X-PLOR>for $image in (1 -1) loop imag FOR LOOP: symbol IMAGE set to -1.00000 (real) X-PLOR> X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates COOR>REMARK FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/dg.pdb" COOR>REMARK DATE:16-Aug-96 18:39:32 created by user: COOR>ATOM 1 P GUA 1 11.985 -3.989 8.809 1.00 0.00 A COOR>ATOM 2 O1P GUA 1 14.459 -6.228 5.905 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 = 2.3495 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.7435 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2770 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.1832 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.3325 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.5138 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.4453 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.3633 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.0366 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.2240 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.5023 R.m.s. diff. between fitted set and comp. set for selected atoms = 3.1185 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.9163 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.7883 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2953 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.4048 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9551 R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9030 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.8954 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.0870 R.m.s. diff. between fitted set and comp. set for selected atoms = 2.6756 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 14687 intra-atom interactions NBONDS: found 14759 intra-atom interactions NBONDS: found 14871 intra-atom interactions NBONDS: found 14959 intra-atom interactions NBONDS: found 15191 intra-atom interactions NBONDS: found 15344 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =114086.745 grad(E)=326.566 E(BOND)=13544.576 E(VDW )=9598.273 | | E(CDIH)=4878.881 E(NOE )=85370.746 E(PLAN)=694.268 | ------------------------------------------------------------------------------- NBONDS: found 15503 intra-atom interactions NBONDS: found 15548 intra-atom interactions NBONDS: found 15559 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0002 ----------------------- | Etotal =64913.360 grad(E)=186.110 E(BOND)=5206.272 E(VDW )=7665.900 | | E(CDIH)=3925.810 E(NOE )=47612.693 E(PLAN)=502.685 | ------------------------------------------------------------------------------- NBONDS: found 15621 intra-atom interactions NBONDS: found 15638 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0002 ----------------------- | Etotal =46412.761 grad(E)=111.665 E(BOND)=2019.313 E(VDW )=5597.412 | | E(CDIH)=2923.933 E(NOE )=35519.373 E(PLAN)=352.730 | ------------------------------------------------------------------------------- NBONDS: found 15629 intra-atom interactions NBONDS: found 15566 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0002 ----------------------- | Etotal =37752.043 grad(E)=103.191 E(BOND)=1748.598 E(VDW )=4098.655 | | E(CDIH)=2784.817 E(NOE )=28811.792 E(PLAN)=308.182 | ------------------------------------------------------------------------------- NBONDS: found 15539 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =32201.955 grad(E)=62.499 E(BOND)=987.291 E(VDW )=3392.979 | | E(CDIH)=2790.754 E(NOE )=24729.982 E(PLAN)=300.950 | ------------------------------------------------------------------------------- NBONDS: found 15496 intra-atom interactions NBONDS: found 15408 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0000 ----------------------- | Etotal =28865.722 grad(E)=73.098 E(BOND)=1197.588 E(VDW )=2931.380 | | E(CDIH)=2721.436 E(NOE )=21708.894 E(PLAN)=306.424 | ------------------------------------------------------------------------------- NBONDS: found 15324 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0000 ----------------------- | Etotal =24059.774 grad(E)=69.211 E(BOND)=820.945 E(VDW )=2238.176 | | E(CDIH)=2042.385 E(NOE )=18649.842 E(PLAN)=308.425 | ------------------------------------------------------------------------------- NBONDS: found 15254 intra-atom interactions NBONDS: found 15170 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0000 ----------------------- | Etotal =20856.777 grad(E)=61.841 E(BOND)=735.696 E(VDW )=1755.355 | | E(CDIH)=1739.350 E(NOE )=16323.910 E(PLAN)=302.465 | ------------------------------------------------------------------------------- NBONDS: found 15131 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0000 ----------------------- | Etotal =18633.882 grad(E)=43.772 E(BOND)=455.640 E(VDW )=1497.335 | | E(CDIH)=1489.367 E(NOE )=14897.445 E(PLAN)=294.096 | ------------------------------------------------------------------------------- NBONDS: found 15020 intra-atom interactions NBONDS: found 15105 intra-atom interactions NBONDS: found 15049 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =16843.938 grad(E)=48.715 E(BOND)=562.592 E(VDW )=1286.495 | | E(CDIH)=1351.329 E(NOE )=13409.292 E(PLAN)=234.231 | ------------------------------------------------------------------------------- --------------- cycle= 110 ------ stepsize= 0.0000 ----------------------- | Etotal =16660.028 grad(E)=40.319 E(BOND)=468.157 E(VDW )=1259.152 | | E(CDIH)=1503.444 E(NOE )=13202.767 E(PLAN)=226.507 | ------------------------------------------------------------------------------- --------------- cycle= 120 ------ stepsize= 0.0000 ----------------------- | Etotal =16691.308 grad(E)=42.350 E(BOND)=468.278 E(VDW )=1259.080 | | E(CDIH)=1535.365 E(NOE )=13202.104 E(PLAN)=226.481 | ------------------------------------------------------------------------------- --------------- cycle= 130 ------ stepsize= 0.0000 ----------------------- | Etotal =16691.311 grad(E)=42.350 E(BOND)=468.278 E(VDW )=1259.080 | | E(CDIH)=1535.365 E(NOE )=13202.107 E(PLAN)=226.481 | ------------------------------------------------------------------------------- --------------- cycle= 140 ------ stepsize= 0.0000 ----------------------- | Etotal =16691.311 grad(E)=42.350 E(BOND)=468.278 E(VDW )=1259.080 | | E(CDIH)=1535.365 E(NOE )=13202.107 E(PLAN)=226.481 | ------------------------------------------------------------------------------- %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 15040 intra-atom interactions NBONDS: found 14956 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =109050.977 grad(E)=314.578 E(BOND)=12230.069 E(ANGL)=73289.699 | | E(VDW )=2954.153 E(CDIH)=2791.116 E(NOE )=17268.762 E(PLAN)=517.179 | ------------------------------------------------------------------------------- NBONDS: found 14938 intra-atom interactions NBONDS: found 14968 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0001 ----------------------- | Etotal =74308.511 grad(E)=165.457 E(BOND)=4382.525 E(ANGL)=40533.564 | | E(VDW )=3580.222 E(CDIH)=3168.118 E(NOE )=22079.234 E(PLAN)=564.848 | ------------------------------------------------------------------------------- NBONDS: found 14878 intra-atom interactions NBONDS: found 14877 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0001 ----------------------- | Etotal =61376.302 grad(E)=176.276 E(BOND)=3545.412 E(ANGL)=26697.087 | | E(VDW )=3640.941 E(CDIH)=3512.662 E(NOE )=23333.635 E(PLAN)=646.565 | ------------------------------------------------------------------------------- NBONDS: found 14807 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0001 ----------------------- | Etotal =52183.205 grad(E)=121.000 E(BOND)=2549.379 E(ANGL)=20868.170 | | E(VDW )=2901.737 E(CDIH)=3561.881 E(NOE )=21675.416 E(PLAN)=626.622 | ------------------------------------------------------------------------------- NBONDS: found 14679 intra-atom interactions NBONDS: found 14576 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =46144.487 grad(E)=95.279 E(BOND)=2000.613 E(ANGL)=16357.730 | | E(VDW )=2534.993 E(CDIH)=3600.214 E(NOE )=21005.351 E(PLAN)=645.586 | ------------------------------------------------------------------------------- NBONDS: found 14445 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0001 ----------------------- | Etotal =41938.246 grad(E)=78.367 E(BOND)=1774.548 E(ANGL)=13917.988 | | E(VDW )=2271.020 E(CDIH)=3497.117 E(NOE )=19842.796 E(PLAN)=634.778 | ------------------------------------------------------------------------------- NBONDS: found 14299 intra-atom interactions NBONDS: found 14148 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0001 ----------------------- | Etotal =39363.064 grad(E)=63.473 E(BOND)=1633.208 E(ANGL)=11851.070 | | E(VDW )=2263.053 E(CDIH)=3535.053 E(NOE )=19477.110 E(PLAN)=603.570 | ------------------------------------------------------------------------------- NBONDS: found 14083 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0001 ----------------------- | Etotal =36872.110 grad(E)=55.729 E(BOND)=1474.698 E(ANGL)=10428.735 | | E(VDW )=2004.435 E(CDIH)=3524.761 E(NOE )=18871.644 E(PLAN)=567.836 | ------------------------------------------------------------------------------- NBONDS: found 13990 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0001 ----------------------- | Etotal =35141.212 grad(E)=53.881 E(BOND)=1358.639 E(ANGL)=9316.524 | | E(VDW )=1957.211 E(CDIH)=3498.854 E(NOE )=18460.661 E(PLAN)=549.322 | ------------------------------------------------------------------------------- NBONDS: found 13892 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =33898.949 grad(E)=37.907 E(BOND)=1230.169 E(ANGL)=8556.615 | | E(VDW )=1972.911 E(CDIH)=3473.138 E(NOE )=18137.450 E(PLAN)=528.666 | ------------------------------------------------------------------------------- NBONDS: found 13867 intra-atom interactions --------------- cycle= 110 ------ stepsize= 0.0001 ----------------------- | Etotal =32859.505 grad(E)=32.719 E(BOND)=1167.422 E(ANGL)=8060.260 | | E(VDW )=1939.721 E(CDIH)=3415.587 E(NOE )=17768.349 E(PLAN)=508.166 | ------------------------------------------------------------------------------- --------------- cycle= 120 ------ stepsize= 0.0001 ----------------------- | Etotal =32257.441 grad(E)=29.241 E(BOND)=1133.416 E(ANGL)=7983.941 | | E(VDW )=1849.173 E(CDIH)=3359.022 E(NOE )=17433.014 E(PLAN)=498.876 | ------------------------------------------------------------------------------- NBONDS: found 13806 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0001 ----------------------- | Etotal =31770.195 grad(E)=33.518 E(BOND)=1146.936 E(ANGL)=7943.728 | | E(VDW )=1729.115 E(CDIH)=3342.983 E(NOE )=17125.003 E(PLAN)=482.430 | ------------------------------------------------------------------------------- NBONDS: found 13713 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0001 ----------------------- | Etotal =31144.513 grad(E)=31.028 E(BOND)=1183.744 E(ANGL)=7658.623 | | E(VDW )=1702.296 E(CDIH)=3283.264 E(NOE )=16848.398 E(PLAN)=468.189 | ------------------------------------------------------------------------------- NBONDS: found 13619 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =30591.910 grad(E)=28.879 E(BOND)=1170.331 E(ANGL)=7485.568 | | E(VDW )=1654.367 E(CDIH)=3242.758 E(NOE )=16586.150 E(PLAN)=452.735 | ------------------------------------------------------------------------------- --------------- cycle= 160 ------ stepsize= 0.0001 ----------------------- | Etotal =30163.115 grad(E)=26.263 E(BOND)=1148.108 E(ANGL)=7243.072 | | E(VDW )=1653.866 E(CDIH)=3257.963 E(NOE )=16428.537 E(PLAN)=431.568 | ------------------------------------------------------------------------------- NBONDS: found 13559 intra-atom interactions --------------- cycle= 170 ------ stepsize= 0.0001 ----------------------- | Etotal =29827.426 grad(E)=24.414 E(BOND)=1126.187 E(ANGL)=7008.767 | | E(VDW )=1664.207 E(CDIH)=3276.807 E(NOE )=16342.114 E(PLAN)=409.344 | ------------------------------------------------------------------------------- NBONDS: found 13475 intra-atom interactions --------------- cycle= 180 ------ stepsize= 0.0001 ----------------------- | Etotal =29424.068 grad(E)=23.330 E(BOND)=1122.355 E(ANGL)=6694.891 | | E(VDW )=1678.345 E(CDIH)=3260.392 E(NOE )=16272.935 E(PLAN)=395.150 | ------------------------------------------------------------------------------- NBONDS: found 13392 intra-atom interactions --------------- cycle= 190 ------ stepsize= 0.0001 ----------------------- | Etotal =28922.868 grad(E)=25.860 E(BOND)=1139.822 E(ANGL)=6385.354 | | E(VDW )=1678.707 E(CDIH)=3213.131 E(NOE )=16120.380 E(PLAN)=385.473 | ------------------------------------------------------------------------------- NBONDS: found 13291 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =28566.841 grad(E)=26.970 E(BOND)=1093.174 E(ANGL)=6304.639 | | E(VDW )=1689.790 E(CDIH)=3182.044 E(NOE )=15918.934 E(PLAN)=378.259 | ------------------------------------------------------------------------------- --------------- cycle= 210 ------ stepsize= 0.0001 ----------------------- | Etotal =28253.479 grad(E)=20.586 E(BOND)=1070.571 E(ANGL)=6161.094 | | E(VDW )=1738.017 E(CDIH)=3191.979 E(NOE )=15720.274 E(PLAN)=371.543 | ------------------------------------------------------------------------------- NBONDS: found 13256 intra-atom interactions --------------- cycle= 220 ------ stepsize= 0.0001 ----------------------- | Etotal =27994.364 grad(E)=22.501 E(BOND)=1079.309 E(ANGL)=6142.625 | | E(VDW )=1671.591 E(CDIH)=3183.064 E(NOE )=15566.366 E(PLAN)=351.409 | ------------------------------------------------------------------------------- NBONDS: found 13151 intra-atom interactions --------------- cycle= 230 ------ stepsize= 0.0001 ----------------------- | Etotal =27740.329 grad(E)=18.674 E(BOND)=1043.983 E(ANGL)=6130.735 | | E(VDW )=1591.223 E(CDIH)=3176.320 E(NOE )=15471.354 E(PLAN)=326.714 | ------------------------------------------------------------------------------- NBONDS: found 13077 intra-atom interactions --------------- cycle= 240 ------ stepsize= 0.0001 ----------------------- | Etotal =27532.335 grad(E)=19.990 E(BOND)=1044.862 E(ANGL)=6088.513 | | E(VDW )=1563.541 E(CDIH)=3190.032 E(NOE )=15333.387 E(PLAN)=312.000 | ------------------------------------------------------------------------------- NBONDS: found 13044 intra-atom interactions --------------- cycle= 250 ------ stepsize= 0.0001 ----------------------- | Etotal =27360.969 grad(E)=18.031 E(BOND)=1025.381 E(ANGL)=6066.209 | | E(VDW )=1572.251 E(CDIH)=3181.736 E(NOE )=15200.135 E(PLAN)=315.258 | ------------------------------------------------------------------------------- --------------- cycle= 260 ------ stepsize= 0.0001 ----------------------- | Etotal =27179.676 grad(E)=17.937 E(BOND)=1033.647 E(ANGL)=6028.231 | | E(VDW )=1578.216 E(CDIH)=3166.251 E(NOE )=15050.406 E(PLAN)=322.925 | ------------------------------------------------------------------------------- NBONDS: found 12988 intra-atom interactions --------------- cycle= 270 ------ stepsize= 0.0001 ----------------------- | Etotal =27034.908 grad(E)=13.756 E(BOND)=1035.316 E(ANGL)=5967.628 | | E(VDW )=1564.018 E(CDIH)=3171.447 E(NOE )=14970.593 E(PLAN)=325.906 | ------------------------------------------------------------------------------- NBONDS: found 12971 intra-atom interactions --------------- cycle= 280 ------ stepsize= 0.0001 ----------------------- | Etotal =26843.127 grad(E)=17.042 E(BOND)=1031.600 E(ANGL)=5894.427 | | E(VDW )=1561.632 E(CDIH)=3166.221 E(NOE )=14863.235 E(PLAN)=326.012 | ------------------------------------------------------------------------------- NBONDS: found 12952 intra-atom interactions --------------- cycle= 290 ------ stepsize= 0.0001 ----------------------- | Etotal =26651.971 grad(E)=19.337 E(BOND)=1043.936 E(ANGL)=5879.886 | | E(VDW )=1548.451 E(CDIH)=3140.667 E(NOE )=14699.127 E(PLAN)=339.905 | ------------------------------------------------------------------------------- --------------- cycle= 300 ------ stepsize= 0.0001 ----------------------- | Etotal =26457.171 grad(E)=18.320 E(BOND)=1055.590 E(ANGL)=5855.457 | | E(VDW )=1489.753 E(CDIH)=3085.050 E(NOE )=14615.914 E(PLAN)=355.408 | ------------------------------------------------------------------------------- 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= 172635945. ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 0.00000 -0.00002 -0.00001 velocity [A/ps] : -0.04760 -0.10801 -0.09965 ang. mom. [amu A/ps] : 194546.11225 119078.53594 83943.26149 kin. ener. [Kcal/mol] : 1.93063 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.00000 -0.00002 -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 12892 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=38638.133 E(kin)=5898.138 temperature=2922.775 | | Etotal =32739.995 grad(E)=89.427 E(BOND)=105.559 E(ANGL)=585.546 | | E(DIHE)=0.000 E(IMPR)=12502.766 E(VDW )=1489.753 E(CDIH)=3085.050 | | E(NOE )=14615.914 E(PLAN)=355.408 | ------------------------------------------------------------------------------- NBONDS: found 12870 intra-atom interactions NBONDS: found 12865 intra-atom interactions NBONDS: found 12796 intra-atom interactions NBONDS: found 12756 intra-atom interactions NBONDS: found 12673 intra-atom interactions NBONDS: found 12619 intra-atom interactions NBONDS: found 12574 intra-atom interactions NBONDS: found 12584 intra-atom interactions NBONDS: found 12557 intra-atom interactions NBONDS: found 12530 intra-atom interactions NBONDS: found 12517 intra-atom interactions NBONDS: found 12491 intra-atom interactions NBONDS: found 12474 intra-atom interactions NBONDS: found 12519 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=33540.939 E(kin)=6804.875 temperature=3372.101 | | Etotal =26736.064 grad(E)=71.070 E(BOND)=3316.569 E(ANGL)=5698.429 | | E(DIHE)=0.000 E(IMPR)=6773.095 E(VDW )=919.923 E(CDIH)=1597.320 | | E(NOE )=8149.298 E(PLAN)=281.430 | ------------------------------------------------------------------------------- NBONDS: found 12468 intra-atom interactions NBONDS: found 12411 intra-atom interactions NBONDS: found 12395 intra-atom interactions NBONDS: found 12370 intra-atom interactions NBONDS: found 12414 intra-atom interactions NBONDS: found 12421 intra-atom interactions NBONDS: found 12404 intra-atom interactions NBONDS: found 12418 intra-atom interactions NBONDS: found 12435 intra-atom interactions NBONDS: found 12445 intra-atom interactions NBONDS: found 12435 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=31272.875 E(kin)=6396.472 temperature=3169.720 | | Etotal =24876.403 grad(E)=70.878 E(BOND)=3150.916 E(ANGL)=5841.300 | | E(DIHE)=0.000 E(IMPR)=5796.584 E(VDW )=953.802 E(CDIH)=1563.156 | | E(NOE )=7253.807 E(PLAN)=316.837 | ------------------------------------------------------------------------------- NBONDS: found 12386 intra-atom interactions NBONDS: found 12347 intra-atom interactions NBONDS: found 12320 intra-atom interactions NBONDS: found 12323 intra-atom interactions NBONDS: found 12307 intra-atom interactions NBONDS: found 12292 intra-atom interactions NBONDS: found 12256 intra-atom interactions NBONDS: found 12272 intra-atom interactions NBONDS: found 12234 intra-atom interactions NBONDS: found 12206 intra-atom interactions NBONDS: found 12242 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=30233.547 E(kin)=6382.468 temperature=3162.781 | | Etotal =23851.079 grad(E)=70.198 E(BOND)=2871.150 E(ANGL)=4927.405 | | E(DIHE)=0.000 E(IMPR)=5971.789 E(VDW )=780.824 E(CDIH)=1615.498 | | E(NOE )=7528.877 E(PLAN)=155.536 | ------------------------------------------------------------------------------- NBONDS: found 12283 intra-atom interactions NBONDS: found 12246 intra-atom interactions NBONDS: found 12249 intra-atom interactions NBONDS: found 12268 intra-atom interactions NBONDS: found 12338 intra-atom interactions NBONDS: found 12396 intra-atom interactions NBONDS: found 12424 intra-atom interactions NBONDS: found 12467 intra-atom interactions NBONDS: found 12472 intra-atom interactions NBONDS: found 12503 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=29092.341 E(kin)=6281.688 temperature=3112.840 | | Etotal =22810.653 grad(E)=64.581 E(BOND)=2775.036 E(ANGL)=4866.598 | | E(DIHE)=0.000 E(IMPR)=5701.706 E(VDW )=846.053 E(CDIH)=1565.727 | | E(NOE )=6953.769 E(PLAN)=101.763 | ------------------------------------------------------------------------------- NBONDS: found 12569 intra-atom interactions NBONDS: found 12584 intra-atom interactions NBONDS: found 12592 intra-atom interactions NBONDS: found 12600 intra-atom interactions NBONDS: found 12655 intra-atom interactions NBONDS: found 12708 intra-atom interactions NBONDS: found 12697 intra-atom interactions NBONDS: found 12703 intra-atom interactions NBONDS: found 12714 intra-atom interactions NBONDS: found 12697 intra-atom interactions NBONDS: found 12642 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=29516.705 E(kin)=6503.306 temperature=3222.661 | | Etotal =23013.399 grad(E)=69.351 E(BOND)=2769.626 E(ANGL)=5061.808 | | E(DIHE)=0.000 E(IMPR)=5679.935 E(VDW )=716.045 E(CDIH)=1590.836 | | E(NOE )=7065.457 E(PLAN)=129.691 | ------------------------------------------------------------------------------- NBONDS: found 12642 intra-atom interactions NBONDS: found 12632 intra-atom interactions NBONDS: found 12593 intra-atom interactions NBONDS: found 12518 intra-atom interactions NBONDS: found 12452 intra-atom interactions NBONDS: found 12388 intra-atom interactions NBONDS: found 12285 intra-atom interactions NBONDS: found 12265 intra-atom interactions NBONDS: found 12199 intra-atom interactions NBONDS: found 12165 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=28655.186 E(kin)=6109.330 temperature=3027.430 | | Etotal =22545.856 grad(E)=66.676 E(BOND)=2847.390 E(ANGL)=4812.749 | | E(DIHE)=0.000 E(IMPR)=5296.065 E(VDW )=499.649 E(CDIH)=1669.532 | | E(NOE )=7298.466 E(PLAN)=122.005 | ------------------------------------------------------------------------------- NBONDS: found 12062 intra-atom interactions NBONDS: found 12036 intra-atom interactions NBONDS: found 12045 intra-atom interactions NBONDS: found 12073 intra-atom interactions NBONDS: found 12033 intra-atom interactions NBONDS: found 12022 intra-atom interactions NBONDS: found 12029 intra-atom interactions NBONDS: found 12052 intra-atom interactions NBONDS: found 12013 intra-atom interactions NBONDS: found 12007 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=28860.471 E(kin)=6093.644 temperature=3019.657 | | Etotal =22766.827 grad(E)=67.666 E(BOND)=2871.307 E(ANGL)=5143.363 | | E(DIHE)=0.000 E(IMPR)=5050.247 E(VDW )=734.682 E(CDIH)=1494.308 | | E(NOE )=7354.335 E(PLAN)=118.584 | ------------------------------------------------------------------------------- NBONDS: found 12022 intra-atom interactions NBONDS: found 12042 intra-atom interactions NBONDS: found 12052 intra-atom interactions NBONDS: found 12078 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00000 -0.00002 -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 -0.00002 -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 -0.00002 -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 12059 intra-atom interactions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=41626.586 E(kin)=6226.181 temperature=3085.334 | | Etotal =35400.405 grad(E)=124.595 E(BOND)=5432.812 E(ANGL)=10198.446 | | E(DIHE)=0.000 E(IMPR)=10278.940 E(VDW )=672.281 E(CDIH)=1446.810 | | E(NOE )=7173.882 E(PLAN)=197.234 | ------------------------------------------------------------------------------- NBONDS: found 12111 intra-atom interactions NBONDS: found 12116 intra-atom interactions NBONDS: found 12150 intra-atom interactions NBONDS: found 12183 intra-atom interactions NBONDS: found 12253 intra-atom interactions NBONDS: found 12223 intra-atom interactions NBONDS: found 12201 intra-atom interactions NBONDS: found 12212 intra-atom interactions NBONDS: found 12195 intra-atom interactions NBONDS: found 12186 intra-atom interactions --------------- step= 100 at 0.20000 ps -------------------------------- | E(kin)+E(total)=36808.746 E(kin)=7020.350 temperature=3478.878 | | Etotal =29788.396 grad(E)=94.290 E(BOND)=2914.294 E(ANGL)=7077.814 | | E(DIHE)=0.000 E(IMPR)=8260.026 E(VDW )=1180.604 E(CDIH)=1599.815 | | E(NOE )=8573.907 E(PLAN)=181.937 | ------------------------------------------------------------------------------- NBONDS: found 12189 intra-atom interactions NBONDS: found 12191 intra-atom interactions NBONDS: found 12194 intra-atom interactions NBONDS: found 12172 intra-atom interactions NBONDS: found 12186 intra-atom interactions NBONDS: found 12230 intra-atom interactions NBONDS: found 12231 intra-atom interactions NBONDS: found 12213 intra-atom interactions NBONDS: found 12216 intra-atom interactions NBONDS: found 12243 intra-atom interactions NBONDS: found 12295 intra-atom interactions --------------- step= 200 at 0.40000 ps -------------------------------- | E(kin)+E(total)=34501.723 E(kin)=6728.719 temperature=3334.363 | | Etotal =27773.004 grad(E)=90.407 E(BOND)=2891.630 E(ANGL)=6408.513 | | E(DIHE)=0.000 E(IMPR)=7529.328 E(VDW )=1141.734 E(CDIH)=1518.284 | | E(NOE )=8173.465 E(PLAN)=110.051 | ------------------------------------------------------------------------------- NBONDS: found 12291 intra-atom interactions NBONDS: found 12295 intra-atom interactions NBONDS: found 12265 intra-atom interactions NBONDS: found 12268 intra-atom interactions NBONDS: found 12304 intra-atom interactions NBONDS: found 12282 intra-atom interactions NBONDS: found 12337 intra-atom interactions NBONDS: found 12325 intra-atom interactions NBONDS: found 12355 intra-atom interactions NBONDS: found 12385 intra-atom interactions NBONDS: found 12424 intra-atom interactions NBONDS: found 12437 intra-atom interactions NBONDS: found 12448 intra-atom interactions NBONDS: found 12453 intra-atom interactions --------------- step= 300 at 0.60000 ps -------------------------------- | E(kin)+E(total)=33250.938 E(kin)=6006.756 temperature=2976.600 | | Etotal =27244.182 grad(E)=102.839 E(BOND)=2800.964 E(ANGL)=6264.468 | | E(DIHE)=0.000 E(IMPR)=7608.816 E(VDW )=995.104 E(CDIH)=1495.686 | | E(NOE )=7967.694 E(PLAN)=111.449 | ------------------------------------------------------------------------------- NBONDS: found 12478 intra-atom interactions NBONDS: found 12520 intra-atom interactions NBONDS: found 12525 intra-atom interactions NBONDS: found 12551 intra-atom interactions NBONDS: found 12548 intra-atom interactions NBONDS: found 12574 intra-atom interactions NBONDS: found 12535 intra-atom interactions NBONDS: found 12511 intra-atom interactions NBONDS: found 12518 intra-atom interactions NBONDS: found 12491 intra-atom interactions --------------- step= 400 at 0.80000 ps -------------------------------- | E(kin)+E(total)=32707.023 E(kin)=6321.130 temperature=3132.385 | | Etotal =26385.893 grad(E)=90.352 E(BOND)=2884.054 E(ANGL)=6546.933 | | E(DIHE)=0.000 E(IMPR)=6708.468 E(VDW )=985.725 E(CDIH)=1607.162 | | E(NOE )=7496.519 E(PLAN)=157.031 | ------------------------------------------------------------------------------- NBONDS: found 12486 intra-atom interactions NBONDS: found 12515 intra-atom interactions NBONDS: found 12490 intra-atom interactions NBONDS: found 12464 intra-atom interactions NBONDS: found 12457 intra-atom interactions NBONDS: found 12410 intra-atom interactions NBONDS: found 12450 intra-atom interactions NBONDS: found 12436 intra-atom interactions NBONDS: found 12441 intra-atom interactions NBONDS: found 12475 intra-atom interactions --------------- step= 500 at 1.00000 ps -------------------------------- | E(kin)+E(total)=31809.322 E(kin)=6225.659 temperature=3085.075 | | Etotal =25583.663 grad(E)=88.240 E(BOND)=2846.256 E(ANGL)=6104.051 | | E(DIHE)=0.000 E(IMPR)=6666.314 E(VDW )=844.418 E(CDIH)=1391.678 | | E(NOE )=7596.409 E(PLAN)=134.538 | ------------------------------------------------------------------------------- NBONDS: found 12476 intra-atom interactions NBONDS: found 12445 intra-atom interactions NBONDS: found 12514 intra-atom interactions NBONDS: found 12520 intra-atom interactions NBONDS: found 12536 intra-atom interactions NBONDS: found 12548 intra-atom interactions NBONDS: found 12521 intra-atom interactions NBONDS: found 12537 intra-atom interactions NBONDS: found 12542 intra-atom interactions --------------- step= 600 at 1.20000 ps -------------------------------- | E(kin)+E(total)=31404.265 E(kin)=6080.246 temperature=3013.017 | | Etotal =25324.019 grad(E)=90.325 E(BOND)=2868.043 E(ANGL)=6161.630 | | E(DIHE)=0.000 E(IMPR)=6553.224 E(VDW )=997.746 E(CDIH)=1496.172 | | E(NOE )=7163.242 E(PLAN)=83.960 | ------------------------------------------------------------------------------- NBONDS: found 12503 intra-atom interactions NBONDS: found 12501 intra-atom interactions NBONDS: found 12596 intra-atom interactions NBONDS: found 12620 intra-atom interactions NBONDS: found 12644 intra-atom interactions NBONDS: found 12637 intra-atom interactions NBONDS: found 12649 intra-atom interactions NBONDS: found 12705 intra-atom interactions NBONDS: found 12782 intra-atom interactions --------------- step= 700 at 1.40000 ps -------------------------------- | E(kin)+E(total)=30942.669 E(kin)=6090.743 temperature=3018.219 | | Etotal =24851.926 grad(E)=89.839 E(BOND)=2680.006 E(ANGL)=6226.913 | | E(DIHE)=0.000 E(IMPR)=6942.618 E(VDW )=635.862 E(CDIH)=1343.718 | | E(NOE )=6888.988 E(PLAN)=133.820 | ------------------------------------------------------------------------------- NBONDS: found 12843 intra-atom interactions NBONDS: found 12923 intra-atom interactions NBONDS: found 13032 intra-atom interactions NBONDS: found 13066 intra-atom interactions CENMAS: Information about center of free masses position [A] : 0.00000 -0.00002 -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 -0.00002 -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 -0.00002 -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 retriev