X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=examples%2Funres%2FMD%2Fmicrocanonical%2FDYN_SS%2Foutputs%2Fsmall.out_GB000;fp=examples%2Funres%2FMD%2Fmicrocanonical%2FDYN_SS%2Foutputs%2Fsmall.out_GB000;h=9904891d5b005fc577bda78d027ccd083bf2688e;hp=0000000000000000000000000000000000000000;hb=2a226bfc86eabc6e4eae0c3ad1cbc3cb5417a05a;hpb=a0e685f844163003749ba91dfbf4644bcc8cfa30 diff --git a/examples/unres/MD/microcanonical/DYN_SS/outputs/small.out_GB000 b/examples/unres/MD/microcanonical/DYN_SS/outputs/small.out_GB000 new file mode 100644 index 0000000..9904891 --- /dev/null +++ b/examples/unres/MD/microcanonical/DYN_SS/outputs/small.out_GB000 @@ -0,0 +1,427 @@ +-------------------------------------------------------------------------------- + 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