-------------------------------------------------------------------------------- FILE ASSIGNMENT -------------------------------------------------------------------------------- Input file : small.inp Output file : small.out_GB000 Sidechain potential file : /users/czarek/UNRES/GIT/unres/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16- 10-8k SCp potential file : /users/czarek/UNRES/GIT/unres/PARAM/scp.parm Electrostatic potential file : /users/czarek/UNRES/GIT/unres/PARAM/electr_631Gdp.parm Cumulant coefficient file : /users/czarek/UNRES/GIT/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3 Torsional parameter file : /users/czarek/UNRES/GIT/unres/PARAM/torsion_631Gdp.parm Double torsional parameter file : /users/czarek/UNRES/GIT/unres/PARAM/torsion_double_631Gdp.parm SCCOR parameter file : /users/czarek/UNRES/GIT/unres/PARAM/sccor_pdb_shelly.dat Bond & inertia constant file : /users/czarek/UNRES/GIT/unres/PARAM/bond.parm Bending parameter file : /users/czarek/UNRES/GIT/unres/PARAM/thetaml.5parm Rotamer parameter file : /users/czarek/UNRES/GIT/unres/PARAM/scgauss.parm Threading database : /users/czarek/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 52 compiled Sun Feb 17 00:55:22 2013 compiled by czarek@piasek3 OS name: Linux OS release: 2.6.32-42-generic OS version: #96-Ubuntu SMP Wed Aug 15 19:37:37 UTC 2012 flags: INSTALL_DIR = /users/software/mpich-1.2.7p1_int... FC= ifort OPT = -O3 -ip FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include FFLAGS1 = -c -g -CA -CB -I$(INSTALL_DIR)/inclu... FFLAGS2 = -c -g -O0 -I$(INSTALL_DIR)/include FFLAGSE = -c -O3 -ipo -opt_report -I$(INSTALL... LIBS = -L$(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 -16 -62756 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: 100000 Initial time step of numerical integration: 0.01000 natural units 0.48900 fs Maximum acceleration threshold to reduce the time step/increase split number: 5.00000 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: 100 Frequency of coordinate output: 500 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 11.1621168104436 AKTH 8.13134337184633 AKCT 8.87055640565054 V1SS -0.798350076508549 V2SS 5.62541118725005 V3SS 10.1272185631177 EBR -5.50000000000000 SS_DEPTH -5.46701011744817 HT -1.40133843152500 PDB data will be read from file a.pdb Nres: 18 Backbone and SC coordinates as read from the PDB 1 10 GLY -11.849 6.596 -2.403 -11.849 6.596 -2.403 2 9 ALA -13.418 6.572 -5.919 -12.908 6.747 -6.410 3 9 ALA -16.143 3.889 -6.138 -16.793 4.183 -6.397 4 9 ALA -13.520 1.166 -6.550 -12.785 1.239 -6.559 5 1 CYS -12.629 1.631 -2.805 -13.518 2.576 -2.698 6 9 ALA -13.467 -2.136 -2.650 -13.490 -2.860 -2.729 7 9 ALA -11.256 -2.842 -5.622 -11.072 -2.578 -6.320 8 9 ALA -8.206 -2.125 -3.496 -8.226 -1.485 -3.216 9 9 ALA -9.298 -4.587 -0.877 -9.634 -4.348 -0.224 10 9 ALA -10.565 -6.979 -3.578 -10.220 -7.012 -4.281 11 9 ALA -9.060 -10.399 -3.347 -9.290 -11.104 -3.486 12 9 ALA -5.538 -8.995 -3.201 -5.545 -8.635 -3.863 13 9 ALA -4.176 -7.434 -0.023 -3.823 -8.014 0.272 14 1 CYS -3.957 -3.989 1.621 -5.048 -3.526 1.725 15 9 ALA -3.473 -3.009 5.302 -3.003 -3.112 5.889 16 9 ALA -3.888 0.809 5.844 -4.524 1.149 5.521 17 9 ALA -3.394 0.685 9.610 -2.879 0.254 9.328 18 10 GLY -3.341 3.372 12.241 -3.341 3.372 12.241 nsup= 18 nstart_sup= 1 After sideadd Geometry of the virtual chain. Res d Theta Gamma Dsc Alpha Beta GLY 1 0.000 0.000 0.000 0.000 0.000 0.000 ALA 2 3.850 0.000 0.000 0.729 146.694 -109.363 ALA 3 3.830 110.272 0.000 0.759 147.957 -128.746 ALA 4 3.803 90.977 -78.713 0.739 105.672 -50.865 CYS 5 3.878 88.166 72.402 1.302 112.139 -116.564 ALA 6 3.862 82.642 123.024 0.729 120.951 3.720 ALA 7 3.771 91.361 49.351 0.769 137.392 -55.570 ALA 8 3.786 89.674 70.311 0.699 119.648 -87.119 ALA 9 3.757 91.902 53.321 0.772 145.673 -99.574 ALA 10 3.824 90.793 38.471 0.784 108.765 -64.768 ALA 11 3.744 113.246 124.426 0.754 167.686 -74.150 ALA 12 3.794 92.149 -50.745 0.754 133.580 -108.877 ALA 13 3.794 121.181 76.519 0.740 168.142 -147.575 CYS 14 3.823 138.722 -91.423 1.190 108.677 -76.446 ALA 15 3.840 130.494 158.051 0.759 141.443 -47.832 ALA 16 3.879 111.821 -172.250 0.790 136.439 -94.007 ALA 17 3.800 95.305 177.774 0.728 120.497 -127.361 GLY 18 3.761 132.203 178.798 0.000 0.000 0.000 ITEL 1 10 1 2 9 1 3 9 1 4 9 1 5 1 1 6 9 1 7 9 1 8 9 1 9 9 1 10 9 1 11 9 1 12 9 1 13 9 1 14 1 1 15 9 1 16 9 1 17 9 1 ns= 2 iss: 5 14 nss= 0 ihpb,jhpb: Boundaries in phi angle sampling: GLY 1 -180.0 180.0 ALA 2 -180.0 180.0 ALA 3 -180.0 180.0 ALA 4 -180.0 180.0 CYS 5 -180.0 180.0 ALA 6 -180.0 180.0 ALA 7 -180.0 180.0 ALA 8 -180.0 180.0 ALA 9 -180.0 180.0 ALA 10 -180.0 180.0 ALA 11 -180.0 180.0 ALA 12 -180.0 180.0 ALA 13 -180.0 180.0 CYS 14 -180.0 180.0 ALA 15 -180.0 180.0 ALA 16 -180.0 180.0 ALA 17 -180.0 180.0 GLY 18 -180.0 180.0 NZ_START= 1 NZ_END= 18 IZ_SC= 0 Geometry of the virtual chain. Res d Theta Gamma Dsc Alpha Beta GLY 1 0.000 0.000 0.000 0.000 0.000 0.000 ALA 2 3.850 0.000 0.000 0.729 146.694 -109.363 ALA 3 3.830 110.272 0.000 0.759 147.957 -128.746 ALA 4 3.803 90.977 -78.713 0.739 105.672 -50.865 CYS 5 3.878 88.166 72.402 1.302 112.139 -116.564 ALA 6 3.862 82.642 123.024 0.729 120.951 3.720 ALA 7 3.771 91.361 49.351 0.769 137.392 -55.570 ALA 8 3.786 89.674 70.311 0.699 119.648 -87.119 ALA 9 3.757 91.902 53.321 0.772 145.673 -99.574 ALA 10 3.824 90.793 38.471 0.784 108.765 -64.768 ALA 11 3.744 113.246 124.426 0.754 167.686 -74.150 ALA 12 3.794 92.149 -50.745 0.754 133.580 -108.877 ALA 13 3.794 121.181 76.519 0.740 168.142 -147.575 CYS 14 3.823 138.722 -91.423 1.190 108.677 -76.446 ALA 15 3.840 130.494 158.051 0.759 141.443 -47.832 ALA 16 3.879 111.821 -172.250 0.790 136.439 -94.007 ALA 17 3.800 95.305 177.774 0.728 120.497 -127.361 GLY 18 3.761 132.203 178.798 0.000 0.000 0.000 The chain contains 2 disulfide-bridging cysteines. 5 14 Running with dynamic disulfide-bond formation Processor 0 CG group 0 absolute rank 0 nhpb 0 link_start= 1 link_end 0 ******************************************************************************** Processor 0: end reading molecular data. ******************************************************************************** Mesoscopic molecular dynamics (MD) calculation. ******************************************************************************** Calling chainbuild ====================MD calculation start==================== Initial velocities randomly generated Initial velocities 0 0.33890 0.02320 0.23659 0.00000 0.00000 0.00000 1 -0.15077 -0.23023 -0.18811 0.00000 0.00000 0.00000 2 -0.14850 0.36395 0.17819 -0.06593 0.14268 0.01033 3 -0.01216 -0.31272 -0.40265 -0.27199 0.03880 -0.26248 4 0.13139 0.25689 0.25345 -0.06906 0.09806 0.19560 5 -0.27858 -0.01261 0.04461 -0.15425 -0.01325 -0.02214 6 0.09914 0.11979 0.14915 -0.11171 -0.17646 -0.10207 7 -0.15740 -0.32760 -0.08342 -0.15559 -0.17162 -0.27142 8 -0.01757 0.19689 -0.31981 -0.04208 0.07236 -0.23178 9 0.29843 -0.21826 0.12725 0.01235 -0.10442 -0.18484 10 -0.35680 0.17980 -0.11210 -0.00509 -0.02006 0.01600 11 0.42311 -0.07463 0.22371 0.30508 -0.03813 0.04260 12 -0.28440 -0.17000 -0.23671 -0.06923 -0.11283 -0.12729 13 0.12013 0.21611 0.14782 0.07641 0.09993 0.18719 14 0.15808 0.02556 -0.12952 -0.10167 -0.08786 -0.15044 15 -0.16543 -0.08643 0.20762 0.03124 -0.00978 0.12744 16 0.07008 0.14536 -0.28387 0.01006 0.26396 -0.15863 17 -0.12394 -0.22493 0.30015 -0.38318 -0.15223 0.30217 18 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 Calling the zero-angular momentum subroutine vcm right after adjustment: 5.424257488318338E-018 -6.299137728369682E-018 1.504794012888313E-017 alpha-carbon coordinates centroid coordinates X Y Z X Y Z GLY( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ALA( 2) 3.85027 0.00000 0.00000 4.08973 0.57597 0.37779 ALA( 3) 5.17743 -3.59315 0.00000 5.67699 -3.69784 -0.56169 ALA( 4) 4.50175 -3.91184 3.72914 4.21000 -3.40822 4.18399 CYS( 5) 0.71590 -4.05898 2.90403 0.97457 -3.92549 1.63515 ALA( 6) 0.93933 -7.41535 4.80177 1.02535 -7.94644 5.29318 ALA( 7) 2.75671 -5.77560 7.67023 3.31749 -5.27434 7.82844 ALA( 8) -0.43207 -3.97536 8.63318 -0.68360 -3.58848 8.10834 ALA( 9) -2.36335 -7.19560 8.74835 -2.82423 -7.40238 8.16418 ALA( 10) 0.63437 -8.99997 10.29116 1.13596 -8.62055 10.75890 ALA( 11) -0.16855 -10.69479 13.53118 0.05650 -11.32099 13.88681 ALA( 12) -1.74585 -7.54908 14.95019 -1.14072 -7.10241 14.90335 ALA( 13) -5.21270 -6.43737 13.88410 -5.62232 -6.73606 14.42357 CYS( 14) -6.82468 -4.19410 11.24062 -6.47796 -4.54138 10.15681 ALA( 15) -10.38945 -4.18760 9.81345 -11.11637 -4.14078 10.02669 ALA( 16) -10.73908 -1.74754 6.81896 -10.18707 -1.79179 6.25526 ALA( 17) -14.37866 -2.58026 6.11029 -14.32832 -2.51011 6.83351 GLY( 18) -16.81959 -1.27490 3.56414 -16.81959 -1.27490 3.56414 Geometry of the virtual chain. Res d Theta Gamma Dsc Alpha Beta GLY 1 0.000 0.000 0.000 0.000 0.000 0.000 ALA 2 3.850 0.000 0.000 0.729 146.694 -109.363 ALA 3 3.830 110.272 0.000 0.759 147.957 -128.746 ALA 4 3.803 90.977 -78.713 0.739 105.672 -50.865 CYS 5 3.878 88.166 72.402 1.302 112.139 -116.564 ALA 6 3.862 82.642 123.024 0.729 120.951 3.720 ALA 7 3.771 91.361 49.351 0.769 137.392 -55.570 ALA 8 3.786 89.674 70.311 0.699 119.648 -87.119 ALA 9 3.757 91.902 53.321 0.772 145.673 -99.574 ALA 10 3.824 90.793 38.471 0.784 108.765 -64.768 ALA 11 3.744 113.246 124.426 0.754 167.686 -74.150 ALA 12 3.794 92.149 -50.745 0.754 133.580 -108.877 ALA 13 3.794 121.181 76.519 0.740 168.142 -147.575 CYS 14 3.823 138.722 -91.423 1.190 108.677 -76.446 ALA 15 3.840 130.494 158.051 0.759 141.443 -47.832 ALA 16 3.879 111.821 -172.250 0.790 136.439 -94.007 ALA 17 3.800 95.305 177.774 0.728 120.497 -127.361 GLY 18 3.761 132.203 178.798 0.000 180.000 180.000 Potential energy and its components Virtual-chain energies: EVDW= -3.681888E+01 WEIGHT= 1.352790E+00 (SC-SC) EVDW2= 2.935543E+01 WEIGHT= 1.593040E+00 (SC-p) EES= -5.873651E+01 WEIGHT= 7.153400E-01 (p-p) EVDWPP= -2.078573E+01 WEIGHT= 1.137100E-01 (p-p VDW) ESTR= 1.126963E+01 WEIGHT= 1.000000E+00 (stretching) EBE= -2.163931E+01 WEIGHT= 1.138730E+00 (bending) ESC= 8.185684E+01 WEIGHT= 1.625800E-01 (SC local) ETORS= 1.409747E+01 WEIGHT= 1.985990E+00 (torsional) ETORSD= 3.856076E-01 WEIGHT= 1.570690E+00 (double torsional) EHPB= 0.000000E+00 WEIGHT= 1.000000E+00 (SS bridges & dist. cnstr.) ECORR4= -3.806576E+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= 5.874355E+00 WEIGHT= 1.603600E-01 (electrostatic-local) ETURN3= 1.472773E+01 WEIGHT= 1.687220E+00 (turns, 3rd order) ETURN4= -3.305062E+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= -1.160756E+01 (total) Initial: Kinetic energy 2.82436E+01 potential energy -1.16076E+01 total energy 1.66360E+01 maximum acceleration 1.95619E+00 SSBOND_FORM 129.12 300.0 5 14 SSBOND_BREAK 134.81 300.0 5 14 SSBOND_FORM 178.26 300.0 5 14 SSBOND_BREAK 180.34 300.0 5 14 SSBOND_FORM 253.52 300.0 5 14 SSBOND_BREAK 258.40 300.0 5 14 SSBOND_FORM 420.52 300.0 5 14 SSBOND_BREAK 421.60 300.0 5 14 SSBOND_FORM 425.82 300.0 5 14 SSBOND_BREAK 428.19 300.0 5 14 SSBOND_FORM 494.06 300.0 5 14 SSBOND_BREAK 496.25 300.0 5 14 SSBOND_FORM 500.25 300.0 5 14 SSBOND_BREAK 500.33 300.0 5 14 SSBOND_FORM 500.82 300.0 5 14 SSBOND_BREAK 501.09 300.0 5 14 SSBOND_FORM 520.74 300.0 5 14 SSBOND_BREAK 570.42 300.0 5 14 SSBOND_FORM 628.51 300.0 5 14 SSBOND_BREAK 630.04 300.0 5 14 SSBOND_FORM 634.06 300.0 5 14 SSBOND_BREAK 638.66 300.0 5 14 SSBOND_FORM 660.47 300.0 5 14 SSBOND_BREAK 661.56 300.0 5 14 SSBOND_FORM 671.40 300.0 5 14 SSBOND_BREAK 673.68 300.0 5 14 SSBOND_FORM 697.08 300.0 5 14 SSBOND_BREAK 699.21 300.0 5 14 SSBOND_FORM 699.76 300.0 5 14 SSBOND_BREAK 700.73 300.0 5 14 SSBOND_FORM 711.03 300.0 5 14 SSBOND_BREAK 713.24 300.0 5 14 SSBOND_FORM 714.76 300.0 5 14 SSBOND_BREAK 717.99 300.0 5 14 SSBOND_FORM 724.88 300.0 5 14 SSBOND_BREAK 749.39 300.0 5 14 SSBOND_FORM 789.73 300.0 5 14 SSBOND_BREAK 793.20 300.0 5 14 =================================== Timing =================================== MD calculations setup: 7.81250E-03 Energy & gradient evaluation: 1.83398E+01 Stochastic MD setup: 0.00000E+00 Stochastic MD step setup: 0.00000E+00 MD steps: 2.24727E+01 ============================ End of MD calculation =========================== CG processor 0 is finishing work. Total wall clock time 22.5898437500000 sec