X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=examples%2Funres%2Fnew%2Fmicrocanonical%2FVTS%2Fff_gab%2F1L2Y_micro.out_GB000;fp=examples%2Funres%2Fnew%2Fmicrocanonical%2FVTS%2Fff_gab%2F1L2Y_micro.out_GB000;h=0000000000000000000000000000000000000000;hp=88e6ca17080d3edce2ac8f8dbfeeb4951244fa68;hb=2a226bfc86eabc6e4eae0c3ad1cbc3cb5417a05a;hpb=a0e685f844163003749ba91dfbf4644bcc8cfa30 diff --git a/examples/unres/new/microcanonical/VTS/ff_gab/1L2Y_micro.out_GB000 b/examples/unres/new/microcanonical/VTS/ff_gab/1L2Y_micro.out_GB000 deleted file mode 100644 index 88e6ca1..0000000 --- a/examples/unres/new/microcanonical/VTS/ff_gab/1L2Y_micro.out_GB000 +++ /dev/null @@ -1,406 +0,0 @@ --------------------------------------------------------------------------------- - 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.1e0g-52-17k-2k-newclass-shan1e9_ga - p8g-sc - 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 2.5 build 302 - compiled Mon Jul 23 17:42:12 2012 - compiled by jal47@matrix.chem.cornell.edu - OS name: Linux - OS release: 2.6.34.9-69.fc13.x86_64 - OS version: #1 SMP Tue May 3 09:23:03 UTC 2011 - flags: - INSTALL_DIR = /users/software/mpich-1.2.7p1_int... - FC= ifort - OPT = -g -ip -w -CB - FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include - FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)... - FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include - FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ... - LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr... - ARCH = LINUX - PP = /lib/cpp -P - object = unres.o arcos.o cartprint.o chainbuild... - GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ... - GAB: BIN = ../../../bin/unres/MD/unres_ifort_MP... - E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR... - E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort... - ++++ 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 -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: - 7.350442094070002E-018 -1.983088023295969E-017 2.245968417632500E-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 0.000 180.000 180.000 -GLY 12 3.800 101.862 -72.814 0.000 180.000 180.000 -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 0.000 180.000 180.000 -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 0.000 180.000 180.000 - Potential energy and its components - -Virtual-chain energies: - -EVDW= -4.436790E+01 WEIGHT= 1.352790D+00 (SC-SC) -EVDW2= 5.228224E+01 WEIGHT= 1.593040D+00 (SC-p) -EES= -1.132072E+02 WEIGHT= 7.153400D-01 (p-p) -EVDWPP= 2.375178E+01 WEIGHT= 1.137100D-01 (p-p VDW) -ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching) -EBE= -1.651995E+01 WEIGHT= 1.138730D+00 (bending) -ESC= 7.185904E+01 WEIGHT= 1.625800D-01 (SC local) -ETORS= 8.243370E+00 WEIGHT= 1.985990D+00 (torsional) -ETORSD= 2.390466E+00 WEIGHT= 1.570690D+00 (double torsional) -EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) -ECORR4= -8.338619E+01 WEIGHT= 4.288700D-01 (multi-body) -ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) -ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) -EELLO= -5.753258E+00 WEIGHT= 1.603600D-01 (electrostatic-local) -ETURN3= 1.901845E+01 WEIGHT= 1.687220D+00 (turns, 3rd order) -ETURN4= -7.304754E+00 WEIGHT= 6.623000D-01 (turns, 4th order) -ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order) -ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+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= -5.145065E+01 (total) - -Initial: - Kinetic energy 3.24616E+01 - potential energy -5.14506E+01 - total energy -1.89891E+01 - - maximum acceleration 1.98994E-01 - - - -=================================== Timing =================================== - - MD calculations setup: 7.81250E-03 - Energy & gradient evaluation: 2.64738E+02 - Stochastic MD setup: 0.00000E+00 - Stochastic MD step setup: 0.00000E+00 - MD steps: 2.96723E+02 - - -============================ End of MD calculation =========================== -CG processor 0 is finishing work. - Total wall clock time 298.832031250000 sec