X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=examples%2Funres%2Fnew%2Fmicrocanonical%2FRESPA%2Fff_1l2y%2F1L2Y_micro.out_GB000;fp=examples%2Funres%2Fnew%2Fmicrocanonical%2FRESPA%2Fff_1l2y%2F1L2Y_micro.out_GB000;h=0000000000000000000000000000000000000000;hp=bb301eff6f581ab41ab39660e3e43cc8739e2c3e;hb=2a226bfc86eabc6e4eae0c3ad1cbc3cb5417a05a;hpb=a0e685f844163003749ba91dfbf4644bcc8cfa30 diff --git a/examples/unres/new/microcanonical/RESPA/ff_1l2y/1L2Y_micro.out_GB000 b/examples/unres/new/microcanonical/RESPA/ff_1l2y/1L2Y_micro.out_GB000 deleted file mode 100644 index bb301ef..0000000 --- a/examples/unres/new/microcanonical/RESPA/ff_1l2y/1L2Y_micro.out_GB000 +++ /dev/null @@ -1,412 +0,0 @@ --------------------------------------------------------------------------------- - FILE ASSIGNMENT --------------------------------------------------------------------------------- - Input file : 1L2Y_micro.inp - Output file : 1L2Y_micro.out_GB000 - - Sidechain potential file : - /users/pk376/unres-git/unres/PARAM/scinter_GB.parm - 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_AM1.parm - Bending parameter file : - /users/pk376/unres-git/unres/PARAM/theta_abinitio.parm - Rotamer parameter file : - /users/pk376/unres-git/unres/PARAM/rotamers_AM1_aura.10022007.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 303 - compiled Mon Jul 23 17:44:56 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 ++++ - Start reading THETA_PDB - End reading THETA_PDB - -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 -A-MTS algorithm used; initial time step for fast-varying short-range forces split into 1 steps. -Short-range force cutoff 2.00 lambda 0.30 -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= 1.000000 (SC-SC) -WSCP= 1.233150 (SC-p) -WELEC= 0.844760 (p-p electr) -WVDWPP= 0.231730 (p-p VDW) -WBOND= 1.000000 (stretching) -WANG= 0.629540 (bending) -WSCLOC= 0.105540 (SC local) -WTOR= 1.843160 (torsional) -WTORD= 1.265710 (double torsional) -WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) -WEL_LOC= 0.373570 (multi-body 3-rd order) -WCORR4= 0.192120 (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= 1.403230 (turns, 3rd order) -WTURN4= 0.646730 (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= 1.000000 (SC-SC) -WSCP= 1.233150 (SC-p) -WELEC= 0.844760 (p-p electr) -WVDWPP= 0.231730 (p-p VDW) -WBOND= 1.000000 (stretching) -WANG= 0.629540 (bending) -WSCLOC= 0.105540 (SC local) -WTOR= 1.843160 (torsional) -WTORD= 1.265710 (double torsional) -WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) -WEL_LOC= 0.373570 (multi-body 3-rd order) -WCORR4= 0.192120 (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= 1.403230 (turns, 3rd order) -WTURN4= 0.646730 (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 - -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 3.861 0.000 0.000 1.977 94.624 -178.093 -LEU 3 3.876 92.239 0.000 2.195 102.878 -79.236 -TYR 4 3.861 92.239 -180.000 3.330 163.195 -7.440 -ILE 5 3.871 90.357 45.849 1.692 144.011 -104.516 -GLN 6 3.846 89.090 55.194 2.338 170.986 -139.318 -TRP 7 3.867 88.657 49.396 3.617 123.650 -21.913 -LEU 8 3.859 93.032 48.298 2.105 151.723 -105.899 -LYS 9 3.882 94.826 46.843 2.997 106.974 -55.960 -ASP 10 3.861 87.966 59.623 1.991 153.447 -128.646 -GLY 11 3.891 89.908 56.679 0.000 0.000 0.000 -GLY 12 3.864 100.181 -87.304 0.000 0.000 0.000 -PRO 13 3.886 109.073 -127.499 1.402 101.771 -115.580 -SER 14 3.876 89.537 4.261 1.267 144.515 -129.218 -SER 15 3.875 91.815 66.108 1.262 161.047 -100.177 -GLY 16 3.866 101.784 70.140 0.000 0.000 0.000 -ARG 17 3.866 92.201 -108.949 3.411 139.846 -132.716 -PRO 18 3.878 133.225 103.824 1.397 115.610 -118.024 -PRO 19 3.860 121.502 -122.527 1.395 118.575 -122.417 -PRO 20 3.858 117.950 -90.285 1.396 118.959 -126.207 -SER 21 3.864 114.201 -108.328 0.708 128.925 -37.341 -D 22 3.858 114.201 180.000 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: - 4.226504204090251E-017 -1.020894735287500E-018 -4.083578941150001E-019 - - - 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) 3.86050 0.00000 0.00000 2.55159 1.47985 0.06557 -LEU( 3) 4.01193 -3.87344 0.00000 3.96088 -4.50305 -2.10206 -TYR( 4) 7.87243 -3.87344 0.00000 10.79652 -4.89021 -1.22632 -ILE( 5) 7.89655 -1.17680 2.77774 7.76075 0.44675 2.31935 -GLN( 6) 5.70141 -3.47509 4.94285 3.60888 -3.02771 5.88565 -TRP( 7) 8.16996 -6.36206 4.22016 10.77228 -8.29798 2.61912 -LEU( 8) 11.25658 -4.20989 5.07405 12.42370 -3.38205 3.52958 -LYS( 9) 9.76612 -2.79308 8.36640 6.86736 -2.82804 9.12493 -ASP( 10) 9.49962 -6.42561 9.64741 7.69328 -7.25489 9.53489 -GLY( 11) 13.31647 -6.90493 9.06335 13.31647 -6.90493 9.06335 -GLY( 12) 13.30671 -8.01769 5.36352 13.30671 -8.01769 5.36352 -PRO( 13) 15.31165 -11.32992 5.02827 16.17763 -10.48298 4.32295 -SER( 14) 15.75414 -11.41497 8.87760 16.77305 -10.71800 9.16233 -SER( 15) 11.95328 -11.92981 9.42670 11.12717 -10.97987 9.51528 -GLY( 16) 11.45094 -15.53878 8.13618 11.45094 -15.53878 8.13618 -ARG( 17) 9.54906 -14.31220 5.00147 7.79760 -12.40573 7.22288 -PRO( 18) 10.53690 -13.94710 1.26956 9.62009 -14.99504 1.15440 -PRO( 19) 10.30439 -10.55356 -0.55592 11.52337 -10.99526 -1.06954 -PRO( 20) 6.99735 -9.68439 -2.34313 7.03150 -8.66136 -1.39345 -SER( 21) 7.20688 -9.78655 -6.20031 7.28380 -10.16020 -6.79638 -D ( 22) 3.89984 -8.91739 -7.98752 3.89984 -8.91739 -7.98752 - -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 3.861 0.000 0.000 1.977 94.624 -178.093 -LEU 3 3.876 92.239 0.000 2.195 102.878 -79.236 -TYR 4 3.861 92.239 -180.000 3.330 163.195 -7.440 -ILE 5 3.871 90.357 45.849 1.692 144.011 -104.516 -GLN 6 3.846 89.090 55.194 2.338 170.986 -139.318 -TRP 7 3.867 88.657 49.396 3.617 123.650 -21.913 -LEU 8 3.859 93.032 48.298 2.105 151.723 -105.899 -LYS 9 3.882 94.826 46.843 2.997 106.974 -55.960 -ASP 10 3.861 87.966 59.623 1.991 153.447 -128.646 -GLY 11 3.891 89.908 56.679 0.000 180.000 180.000 -GLY 12 3.864 100.181 -87.304 0.000 180.000 180.000 -PRO 13 3.886 109.073 -127.499 1.402 101.771 -115.580 -SER 14 3.876 89.537 4.261 1.267 144.515 -129.218 -SER 15 3.875 91.815 66.108 1.262 161.047 -100.177 -GLY 16 3.866 101.784 70.140 0.000 180.000 180.000 -ARG 17 3.866 92.201 -108.949 3.411 139.846 -132.716 -PRO 18 3.878 133.225 103.824 1.397 115.610 -118.024 -PRO 19 3.860 121.502 -122.527 1.395 118.575 -122.417 -PRO 20 3.858 117.950 -90.285 1.396 118.959 -126.207 -SER 21 3.864 114.201 -108.328 0.708 128.925 -37.341 -D 22 3.858 114.201 180.000 0.000 180.000 180.000 - Potential energy and its components - -Virtual-chain energies: - -EVDW= -1.798849E+01 WEIGHT= 1.000000D+00 (SC-SC) -EVDW2= 4.471415E+01 WEIGHT= 1.233150D+00 (SC-p) -EES= -9.165378E+01 WEIGHT= 8.447600D-01 (p-p) -EVDWPP= -3.362882E+01 WEIGHT= 2.317300D-01 (p-p VDW) -ESTR= 5.659036E+01 WEIGHT= 1.000000D+00 (stretching) -EBE= -5.669935E+00 WEIGHT= 6.295400D-01 (bending) -ESC= 1.734458E+02 WEIGHT= 1.055400D-01 (SC local) -ETORS= 1.479510E+01 WEIGHT= 1.843160D+00 (torsional) -ETORSD= 1.006444E+00 WEIGHT= 1.265710D+00 (double torsional) -EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) -ECORR4= -6.528803E+01 WEIGHT= 1.921200D-01 (multi-body) -ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) -ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) -EELLO= -4.012900E+00 WEIGHT= 3.735700D-01 (electrostatic-local) -ETURN3= 1.829789E+01 WEIGHT= 1.403230D+00 (turns, 3rd order) -ETURN4= 6.580750E-01 WEIGHT= 6.467300D-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= 6.386200E+01 (total) - -Initial: - Kinetic energy 3.07644E+01 - potential energy 6.38620E+01 - total energy 9.46264E+01 - - maximum acceleration 1.97191E+00 - - acceleration/energy drift too large 24.8795828613454 - 0.393622871058234 split increased to 2 itime 49077 - itsplit 1 - - -=================================== Timing =================================== - - MD calculations setup: 3.90625E-03 - Energy & gradient evaluation: 3.56734E+02 - Stochastic MD setup: 0.00000E+00 - Stochastic MD step setup: 0.00000E+00 - MD steps: 3.91938E+02 - - -============================ End of MD calculation =========================== -CG processor 0 is finishing work. - Total wall clock time 401.093750000000 sec