X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=examples%2Funres%2FMD%2Fmicrocanonical%2FVTS%2Fff_gab%2Foutputs%2F1L2Y_micro.out_GB000;fp=examples%2Funres%2FMD%2Fmicrocanonical%2FVTS%2Fff_gab%2Foutputs%2F1L2Y_micro.out_GB000;h=f5de123b29e9b89ffe6a5ba6b9cb5b3e8d2ffacc;hp=0000000000000000000000000000000000000000;hb=2a226bfc86eabc6e4eae0c3ad1cbc3cb5417a05a;hpb=a0e685f844163003749ba91dfbf4644bcc8cfa30 diff --git a/examples/unres/MD/microcanonical/VTS/ff_gab/outputs/1L2Y_micro.out_GB000 b/examples/unres/MD/microcanonical/VTS/ff_gab/outputs/1L2Y_micro.out_GB000 new file mode 100644 index 0000000..f5de123 --- /dev/null +++ b/examples/unres/MD/microcanonical/VTS/ff_gab/outputs/1L2Y_micro.out_GB000 @@ -0,0 +1,396 @@ +-------------------------------------------------------------------------------- + FILE ASSIGNMENT +-------------------------------------------------------------------------------- + Input file : 1L2Y_micro.inp + Output file : 1L2Y_micro.out_GB000 + + Sidechain potential file : + /users/pk376/unres-git/unres/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-1 + 0-8k + SCp potential file : /users/pk376/unres-git/unres/PARAM/scp.parm + Electrostatic potential file : + /users/pk376/unres-git/unres/PARAM/electr_631Gdp.parm + Cumulant coefficient file : + /users/pk376/unres-git/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3 + Torsional parameter file : + /users/pk376/unres-git/unres/PARAM/torsion_631Gdp.parm + Double torsional parameter file : + /users/pk376/unres-git/unres/PARAM/torsion_double_631Gdp.parm + SCCOR parameter file : /users/pk376/unres-git/unres/PARAM/sccor_pdb_shelly.dat + Bond & inertia constant file : /users/pk376/unres-git/unres/PARAM/bond.parm + Bending parameter file : + /users/pk376/unres-git/unres/PARAM/thetaml.5parm + Rotamer parameter file : + /users/pk376/unres-git/unres/PARAM/scgauss.parm + Threading database : + /users/pk376/unres-git/unres/PARAM/patterns.cart +-------------------------------------------------------------------------------- +******************************************************************************** +United-residue force field calculation - parallel job. +******************************************************************************** + ### LAST MODIFIED 03/28/12 23:29 by czarek + ++++ Compile info ++++ + Version 3.1 build 0 + Compiled Wed Nov 20 08:38:19 EST 2013 + Compiled by pk376@matrix.chem.cornell.edu + OS name: Linux + OS release: Linux-2.6.34.9-69.fc13.x86_64 + Fortran Compiler: /opt/intel/Compiler/11.1/046/bin + /intel64/ifort + MD Force field: GAB + CPPFLAGS = PROCOR -DUNRES -DISNAN -DSPLITELE -DLAN + G0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DLINUX + -DPGI -DMP -DMPI + ++++ End of compile info ++++ + +Potential is GB , exponents are 6 12 + +Disulfide bridge parameters: +S-S bridge energy: -5.50 +d0cm: 3.78 akcm: 15.10 +akth: 11.00 akct: 12.00 +v1ss: -1.08 v2ss: 7.61 v3ss: 13.70 + MPI: node= 0 iseed(4)= 0 0 -46 + -45086 + ran_num 6.422640197456531E-013 +RMSDBC = 3.0 +RMSDBC1 = 0.5 +RMSDBC1MAX = 1.5 +DRMS = 0.1 +RMSDBCM = 3.0 +Time limit (min): 960.0 + RESCALE_MODE 2 +Library routine used to diagonalize matrices. + +=========================== Parameters of the MD run =========================== + +The units are: +positions: angstrom, time: 48.9 fs +velocity: angstrom/(48.9 fs), acceleration: angstrom/(48.9 fs)**2 +energy: kcal/mol, temperature: K + + Number of time steps: 1000000 + Initial time step of numerical integration: 0.01000 natural units + 0.48900 fs +Maximum acceleration threshold to reduce the time step/increase split number: 20.00000 +Maximum predicted energy drift to reduce the timestep/increase split number: 10.00000 + Maximum velocity threshold to reduce velocities: 20.00000 + Frequency of property output: 10000 + Frequency of coordinate output: 10000 +Microcanonical mode calculation + +============================== End of MD run setup ============================= + + +Energy-term weights (unscaled): + +WSCC= 1.352790 (SC-SC) +WSCP= 1.593040 (SC-p) +WELEC= 0.715340 (p-p electr) +WVDWPP= 0.113710 (p-p VDW) +WBOND= 1.000000 (stretching) +WANG= 1.138730 (bending) +WSCLOC= 0.162580 (SC local) +WTOR= 1.985990 (torsional) +WTORD= 1.570690 (double torsional) +WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) +WEL_LOC= 0.160360 (multi-body 3-rd order) +WCORR4= 0.428870 (multi-body 4th order) +WCORR5= 0.000000 (multi-body 5th order) +WCORR6= 0.000000 (multi-body 6th order) +WSCCOR= 0.000000 (back-scloc correlation) +WTURN3= 1.687220 (turns, 3rd order) +WTURN4= 0.662300 (turns, 4th order) +WTURN6= 0.000000 (turns, 6th order) + +Hydrogen-bonding correlation between contact pairs of peptide groups + +Scaling factor of 1,4 SC-p interactions: 0.400 +General scaling factor of SC-p interactions: 1.000 + +Energy-term weights (scaled): + +WSCC= 1.352790 (SC-SC) +WSCP= 1.593040 (SC-p) +WELEC= 0.715340 (p-p electr) +WVDWPP= 0.113710 (p-p VDW) +WBOND= 1.000000 (stretching) +WANG= 1.138730 (bending) +WSCLOC= 0.162580 (SC local) +WTOR= 1.985990 (torsional) +WTORD= 1.570690 (double torsional) +WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) +WEL_LOC= 0.160360 (multi-body 3-rd order) +WCORR4= 0.428870 (multi-body 4th order) +WCORR5= 0.000000 (multi-body 5th order) +WCORR6= 0.000000 (multi-body 6th order) +WSCCOR= 0.000000 (back-scloc correlatkion) +WTURN3= 1.687220 (turns, 3rd order) +WTURN4= 0.662300 (turns, 4th order) +WTURN6= 0.000000 (turns, 6th order) + Reference temperature for weights calculation: 300.000000000000 + Parameters of the SS-bond potential: + D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH + 11.0000000000000 AKCT 12.0000000000000 + V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS + 13.7000000000000 + EBR -5.50000000000000 SS_DEPTH -7.39571661678271 + HT 0.000000000000000E+000 +PDB data will be read from file ../../../../1L2Y.pdb + Nres: 21 +Backbone and SC coordinates as read from the PDB + 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051 + 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437 + 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850 + 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797 + 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074 + 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853 + 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450 + 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799 + 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146 + 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676 + 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593 + 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723 + 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058 + 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675 + 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546 + 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870 + 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986 + 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688 + 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856 + 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430 + 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488 + 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754 +nsup= 20 nstart_sup= 2 + ITEL + 1 21 0 + 2 14 1 + 3 5 1 + 4 8 1 + 5 4 1 + 6 13 1 + 7 7 1 + 8 5 1 + 9 19 1 + 10 16 1 + 11 10 1 + 12 10 2 + 13 20 1 + 14 12 1 + 15 12 1 + 16 10 1 + 17 18 2 + 18 20 2 + 19 20 2 + 20 20 1 + 21 12 0 + ns= 0 iss: +Boundaries in phi angle sampling: +D 1 -180.0 180.0 +ASN 2 -180.0 180.0 +LEU 3 -180.0 180.0 +TYR 4 -180.0 180.0 +ILE 5 -180.0 180.0 +GLN 6 -180.0 180.0 +TRP 7 -180.0 180.0 +LEU 8 -180.0 180.0 +LYS 9 -180.0 180.0 +ASP 10 -180.0 180.0 +GLY 11 -180.0 180.0 +GLY 12 -180.0 180.0 +PRO 13 -180.0 180.0 +SER 14 -180.0 180.0 +SER 15 -180.0 180.0 +GLY 16 -180.0 180.0 +ARG 17 -180.0 180.0 +PRO 18 -180.0 180.0 +PRO 19 -180.0 180.0 +PRO 20 -180.0 180.0 +SER 21 -180.0 180.0 +D 22 -180.0 180.0 +nsup= 20 + nsup= 20 nstart_sup= 2 nstart_seq= 2 + NZ_START= 2 NZ_END= 21 + IZ_SC= 0 + Contact order: 0.308441558441558 + Shifting contacts: 2 2 + 1 ILE 5 ASN 2 + 2 TRP 7 TYR 4 + 3 LEU 8 TYR 4 + 4 LEU 8 ILE 5 + 5 LYS 9 GLN 6 + 6 GLY 12 TRP 7 + 7 GLY 12 LEU 8 + 8 SER 14 GLY 11 + 9 SER 15 ASP 10 + 10 SER 15 GLY 11 + 11 PRO 19 TRP 7 + 12 PRO 20 LEU 3 + 13 PRO 20 TYR 4 + 14 PRO 20 TRP 7 +Initial geometry will be read in. + +Geometry of the virtual chain. + Res d Theta Gamma Dsc Alpha Beta +D 1 0.000 0.000 0.000 0.000 0.000 0.000 +ASN 2 3.800 0.000 0.000 1.684 102.356 -82.317 +LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685 +TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090 +ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666 +GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945 +TRP 7 3.800 84.466 51.434 2.605 152.178 38.024 +LEU 8 3.800 83.945 53.508 1.939 159.052 179.471 +LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090 +ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797 +GLY 11 3.800 94.602 67.604 0.000 0.000 0.000 +GLY 12 3.800 101.862 -72.814 0.000 0.000 0.000 +PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163 +SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659 +SER 15 3.800 96.264 67.358 1.150 146.290 -130.305 +GLY 16 3.800 138.119 129.701 0.000 0.000 0.000 +ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747 +PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641 +PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.044 +PRO 20 3.800 106.349 -122.306 1.345 93.778 -102.374 +SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303 +D 22 3.800 108.718 92.113 0.000 0.000 0.000 + + +******************************************************************************** + Processor 0: end reading molecular data. +******************************************************************************** + + +Mesoscopic molecular dynamics (MD) calculation. + +******************************************************************************** + + Calling chainbuild +====================MD calculation start==================== + Initial velocities randomly generated + Initial velocities + 0 0.02267 0.06282 -0.18129 0.00000 0.00000 0.00000 + 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 2 -0.36014 -0.22705 -0.00171 -0.06904 -0.02446 0.24778 + 3 0.27655 0.20645 0.14150 0.26200 0.15105 0.09342 + 4 0.10834 -0.11941 0.14712 0.10330 -0.09595 0.03277 + 5 0.05798 -0.08974 0.08325 0.03879 0.02648 -0.14707 + 6 0.01211 0.16444 -0.14711 -0.01628 0.11599 -0.16511 + 7 -0.01010 -0.05513 0.03662 -0.18958 0.06429 0.04531 + 8 -0.01799 0.13439 -0.04510 0.02318 0.10657 0.03722 + 9 -0.26458 -0.01929 0.09531 -0.22533 -0.17075 -0.04594 + 10 0.14062 -0.06051 -0.18363 0.20415 -0.15549 -0.17329 + 11 -0.14145 0.13159 -0.00733 0.00000 0.00000 0.00000 + 12 0.19745 -0.24261 0.01759 0.00000 0.00000 0.00000 + 13 -0.15305 0.28008 0.07251 0.06558 0.14824 0.10057 + 14 0.11104 -0.31941 0.15684 -0.02949 -0.09688 0.05398 + 15 0.14534 0.10342 -0.23754 -0.13923 0.07952 0.07655 + 16 -0.11969 0.14757 0.15002 0.00000 0.00000 0.00000 + 17 -0.09007 -0.15856 -0.20234 -0.07955 -0.08516 -0.10245 + 18 0.24139 0.09063 0.14043 -0.02074 0.10220 0.04907 + 19 -0.14354 -0.07226 -0.29143 -0.12408 -0.06855 -0.02978 + 20 0.28536 0.09023 0.56577 0.02348 0.16297 0.19270 + 21 0.00000 0.00000 0.00000 -0.13725 -0.06434 -0.21957 + 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + Calling the zero-angular momentum subroutine + vcm right after adjustment: + 2.450147364690000E-018 3.126490126817969E-017 6.737905252897502E-018 + + + alpha-carbon coordinates centroid coordinates + X Y Z X Y Z +D ( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 +ASN( 2) 3.80000 0.00000 0.00000 4.19395 0.15176 1.63022 +LEU( 3) 4.77894 -3.67174 0.00000 6.45470 -4.61120 -0.26262 +TYR( 4) 5.40376 -3.34701 3.73419 6.99608 -4.40943 5.31723 +ILE( 5) 1.60715 -3.20688 3.81267 0.66846 -2.00631 2.90072 +GLN( 6) 1.94839 -6.79081 2.59652 1.67496 -6.00460 0.51692 +TRP( 7) 4.28674 -7.18710 5.56554 6.06986 -8.42183 7.00843 +LEU( 8) 1.35234 -5.80840 7.54758 1.66208 -4.14953 8.50254 +LYS( 9) -0.53224 -8.86183 6.29662 0.02805 -9.25716 3.84989 +ASP( 10) 2.43549 -11.11658 7.03737 3.20275 -10.98938 5.51559 +GLY( 11) 2.18504 -10.72111 10.80843 2.18504 -10.72111 10.80843 +GLY( 12) 3.43786 -7.16826 11.30614 3.43786 -7.16826 11.30614 +PRO( 13) 6.99461 -6.28836 10.29851 6.42185 -5.11686 9.96902 +SER( 14) 8.57536 -7.97729 13.31326 8.31540 -7.39705 14.27151 +SER( 15) 7.65918 -11.53050 12.32568 6.78456 -11.09058 11.72234 +GLY( 16) 9.38152 -14.89751 11.95581 9.38152 -14.89751 11.95581 +ARG( 17) 10.03694 -14.62275 8.22286 7.37409 -13.20714 8.38321 +PRO( 18) 12.21420 -12.16088 6.31531 11.85460 -12.99540 5.32369 +PRO( 19) 10.48638 -8.77881 6.18806 11.49173 -8.46972 7.02636 +PRO( 20) 10.10763 -7.90895 2.50840 8.81244 -7.79183 2.85161 +SER( 21) 11.17729 -4.27813 2.17220 10.31507 -3.69519 2.66134 +D ( 22) 14.88269 -4.17086 1.33644 14.88269 -4.17086 1.33644 + +Geometry of the virtual chain. + Res d Theta Gamma Dsc Alpha Beta +D 1 0.000 0.000 0.000 0.000 0.000 0.000 +ASN 2 3.800 0.000 0.000 1.684 102.356 -82.317 +LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685 +TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090 +ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666 +GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945 +TRP 7 3.800 84.466 51.434 2.605 152.178 38.024 +LEU 8 3.800 83.945 53.508 1.939 159.052 179.471 +LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090 +ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797 +GLY 11 3.800 94.602 67.604 0.000 0.000 180.000 +GLY 12 3.800 101.862 -72.814 0.000 0.000 180.000 +PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163 +SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659 +SER 15 3.800 96.264 67.358 1.150 146.290 -130.306 +GLY 16 3.800 138.119 129.701 0.000 0.000 180.000 +ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747 +PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641 +PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.045 +PRO 20 3.800 106.349 -122.306 1.345 93.777 -102.374 +SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303 +D 22 3.800 108.718 92.113 0.000 0.000 180.000 + Potential energy and its components + +Virtual-chain energies: + +EVDW= -4.954316E+01 WEIGHT= 1.352790E+00 (SC-SC) +EVDW2= 5.228224E+01 WEIGHT= 1.593040E+00 (SC-p) +EES= -1.132072E+02 WEIGHT= 7.153400E-01 (p-p) +EVDWPP= 2.375178E+01 WEIGHT= 1.137100E-01 (p-p VDW) +ESTR= 6.779273E-27 WEIGHT= 1.000000E+00 (stretching) +EBE= -1.651995E+01 WEIGHT= 1.138730E+00 (bending) +ESC= 7.185904E+01 WEIGHT= 1.625800E-01 (SC local) +ETORS= 8.243370E+00 WEIGHT= 1.985990E+00 (torsional) +ETORSD= 2.390466E+00 WEIGHT= 1.570690E+00 (double torsional) +EHPB= 0.000000E+00 WEIGHT= 1.000000E+00 (SS bridges & dist. cnstr.) +ECORR4= -8.338619E+01 WEIGHT= 4.288700E-01 (multi-body) +ECORR5= 0.000000E+00 WEIGHT= 0.000000E+00 (multi-body) +ECORR6= 0.000000E+00 WEIGHT= 0.000000E+00 (multi-body) +EELLO= -5.753258E+00 WEIGHT= 1.603600E-01 (electrostatic-local) +ETURN3= 1.901845E+01 WEIGHT= 1.687220E+00 (turns, 3rd order) +ETURN4= -7.304754E+00 WEIGHT= 6.623000E-01 (turns, 4th order) +ETURN6= 0.000000E+00 WEIGHT= 0.000000E+00 (turns, 6th order) +ESCCOR= 0.000000E+00 WEIGHT= 0.000000E+00 (backbone-rotamer corr) +EDIHC= 0.000000E+00 (dihedral angle constraints) +ESS= 0.000000E+00 (disulfide-bridge intrinsic energy) +UCONST= 0.000000E+00 (Constraint energy) +ETOT= -5.845168E+01 (total) + +Initial: + Kinetic energy 3.24616E+01 + potential energy -5.84517E+01 + total energy -2.59901E+01 + + maximum acceleration 2.04223E-01 + + + +=================================== Timing =================================== + + MD calculations setup: 1.17188E-02 + Energy & gradient evaluation: 2.43230E+02 + Stochastic MD setup: 0.00000E+00 + Stochastic MD step setup: 0.00000E+00 + MD steps: 2.62180E+02 + + +============================ End of MD calculation =========================== +CG processor 0 is finishing work. + Total wall clock time 264.281250000000 sec