-------------------------------------------------------------------------------- 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 39 compiled Fri Nov 9 14:19:03 2012 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 -w 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 -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: 5000 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: 1 Frequency of coordinate output: 300 Microcanonical mode calculation ===== Calculation restarted ==== ============================== 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 ss.pdb Nres: 18 Backbone and SC coordinates as read from the PDB 1 10 GLY 18.887 -10.163 -10.608 18.887 -10.163 -10.608 2 9 ALA 18.562 -9.885 -6.834 18.353 -9.134 -6.608 3 9 ALA 16.754 -11.361 -3.915 16.860 -12.098 -3.836 4 9 ALA 16.762 -9.897 -0.433 16.145 -9.572 -0.328 5 1 CYS 15.755 -12.524 2.082 16.051 -13.633 1.487 6 9 ALA 15.104 -12.916 5.816 14.965 -12.382 6.257 7 9 ALA 12.233 -15.298 5.159 11.752 -15.096 4.590 8 9 ALA 12.615 -18.906 4.131 12.996 -18.890 4.861 9 9 ALA 9.909 -21.356 3.181 9.333 -20.985 3.212 10 9 ALA 10.743 -20.954 -0.478 10.850 -20.324 -0.915 11 9 ALA 12.566 -23.869 -1.971 12.731 -24.062 -2.616 12 9 ALA 15.810 -21.927 -1.726 15.774 -21.687 -2.426 13 9 ALA 18.582 -20.075 0.198 19.150 -20.569 0.255 14 1 CYS 19.577 -16.394 -0.296 18.494 -15.682 -0.508 15 9 ALA 22.406 -14.224 1.116 23.137 -14.120 1.199 16 9 ALA 22.651 -10.366 0.632 22.481 -9.688 0.945 17 9 ALA 25.991 -8.590 0.178 26.589 -8.669 0.306 18 10 GLY 26.757 -7.435 -3.316 26.757 -7.435 -3.316 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 3.798 0.000 0.000 0.812 126.829 -76.902 ALA 3 3.737 142.050 0.000 0.749 137.463 -84.306 ALA 4 3.777 124.464 -169.125 0.705 105.294 -78.108 CYS 5 3.774 110.120 -160.528 1.293 158.619 -104.565 ALA 6 3.811 140.379 -177.281 0.706 135.838 -82.329 ALA 7 3.788 91.388 142.499 0.772 126.337 -76.931 ALA 8 3.771 124.902 75.891 0.824 113.900 -118.360 ALA 9 3.772 128.130 -174.931 0.686 107.064 -87.141 ALA 10 3.774 90.943 102.826 0.774 157.826 -59.303 ALA 11 3.748 114.254 105.902 0.693 119.632 -54.909 ALA 12 3.789 89.544 -101.667 0.741 155.157 -110.619 ALA 13 3.849 153.580 60.970 0.755 140.632 -99.009 CYS 14 3.845 125.646 -120.233 1.313 150.049 -92.166 ALA 15 3.835 133.262 -173.688 0.743 134.737 -34.633 ALA 16 3.896 124.125 -171.229 0.766 131.592 -41.437 ALA 17 3.810 122.109 -144.160 0.617 138.711 -49.120 GLY 18 3.759 115.636 105.386 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 3.798 0.000 0.000 0.812 126.829 -76.902 ALA 3 3.737 142.050 0.000 0.749 137.463 -84.306 ALA 4 3.777 124.464 -169.125 0.705 105.294 -78.108 CYS 5 3.774 110.120 -160.528 1.293 158.619 -104.565 ALA 6 3.811 140.379 -177.281 0.706 135.838 -82.329 ALA 7 3.788 91.388 142.499 0.772 126.337 -76.931 ALA 8 3.771 124.902 75.891 0.824 113.900 -118.360 ALA 9 3.772 128.130 -174.931 0.686 107.064 -87.141 ALA 10 3.774 90.943 102.826 0.774 157.826 -59.303 ALA 11 3.748 114.254 105.902 0.693 119.632 -54.909 ALA 12 3.789 89.544 -101.667 0.741 155.157 -110.619 ALA 13 3.849 153.580 60.970 0.755 140.632 -99.009 CYS 14 3.845 125.646 -120.233 1.313 150.049 -92.166 ALA 15 3.835 133.262 -173.688 0.743 134.737 -34.633 ALA 16 3.896 124.125 -171.229 0.766 131.592 -41.437 ALA 17 3.810 122.109 -144.160 0.617 138.711 -49.120 GLY 18 3.759 115.636 105.386 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==================== File small_000.rst does not exist 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: -1.942234132913985E-017 -2.274688624133496E-018 -1.784755689704743E-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) 3.79816 0.00000 0.00000 4.09557 0.41221 0.63276 ALA( 3) 6.74526 -2.29838 0.00000 6.76075 -2.76877 -0.58236 ALA( 4) 10.31159 -1.20121 0.58755 10.49251 -1.37922 1.24552 CYS( 5) 12.70448 -3.80621 -0.72715 12.00677 -4.42453 -1.62291 ALA( 6) 16.44175 -4.52019 -0.93521 16.93092 -4.21944 -0.52386 ALA( 7) 15.86025 -8.21957 -0.36540 15.35081 -8.39881 0.18621 ALA( 8) 14.54201 -10.62082 -2.95704 15.23594 -10.34816 -3.30696 ALA( 9) 13.65028 -14.25975 -2.52064 13.75752 -14.37646 -1.85337 ALA( 10) 9.97261 -13.41422 -2.44808 9.57534 -12.87986 -2.05316 ALA( 11) 8.11976 -14.33184 -5.57450 7.45061 -14.36484 -5.75243 ALA( 12) 8.22776 -10.70552 -6.66675 7.55286 -10.55609 -6.40015 ALA( 13) 10.03788 -7.45810 -7.66343 10.00976 -7.43698 -8.41753 CYS( 14) 9.73131 -4.07719 -5.85807 9.66544 -4.28710 -4.56332 ALA( 15) 11.05109 -0.55921 -6.62480 11.07862 0.01250 -7.09856 ALA( 16) 10.83158 2.44432 -4.15315 11.20676 2.82955 -3.60782 ALA( 17) 10.22466 6.01060 -5.34864 10.29490 6.35777 -5.85338 GLY( 18) 6.77188 7.36501 -4.73819 6.77188 7.36501 -4.73819 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 3.798 0.000 0.000 0.812 126.829 -76.902 ALA 3 3.737 142.050 0.000 0.749 137.463 -84.306 ALA 4 3.777 124.464 -169.125 0.705 105.294 -78.108 CYS 5 3.774 110.120 -160.528 1.293 158.619 -104.565 ALA 6 3.811 140.379 -177.281 0.706 135.838 -82.329 ALA 7 3.788 91.388 142.499 0.772 126.337 -76.931 ALA 8 3.771 124.902 75.891 0.824 113.900 -118.360 ALA 9 3.772 128.130 -174.931 0.686 107.064 -87.141 ALA 10 3.774 90.943 102.826 0.774 157.826 -59.303 ALA 11 3.748 114.254 105.902 0.693 119.632 -54.909 ALA 12 3.789 89.544 -101.667 0.741 155.157 -110.619 ALA 13 3.849 153.580 60.970 0.755 140.632 -99.009 CYS 14 3.845 125.646 -120.233 1.313 150.049 -92.166 ALA 15 3.835 133.262 -173.688 0.743 134.737 -34.633 ALA 16 3.896 124.125 -171.229 0.766 131.592 -41.437 ALA 17 3.810 122.109 -144.160 0.617 138.711 -49.120 GLY 18 3.759 115.636 105.386 0.000 180.000 180.000 SSBOND_E_FORM 0.00 300.0 5 14 dyn_ssbond_ene -4.99323973556562 SSBOND_FORM 0.00 300.0 5 14 Potential energy and its components Virtual-chain energies: EVDW= -3.422318E+01 WEIGHT= 1.352790E+00 (SC-SC) EVDW2= 1.284609E+01 WEIGHT= 1.593040E+00 (SC-p) EES= -1.045287E+01 WEIGHT= 7.153400E-01 (p-p) EVDWPP= -2.004779E+01 WEIGHT= 1.137100E-01 (p-p VDW) ESTR= 1.857136E+01 WEIGHT= 1.000000E+00 (stretching) EBE= -1.634855E+01 WEIGHT= 1.138730E+00 (bending) ESC= 5.355337E+01 WEIGHT= 1.625800E-01 (SC local) ETORS= 8.666828E+00 WEIGHT= 1.985990E+00 (torsional) ETORSD= -6.630800E-01 WEIGHT= 1.570690E+00 (double torsional) EHPB= 0.000000E+00 WEIGHT= 1.000000E+00 (SS bridges & dist. cnstr.) ECORR4= -8.168927E+00 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= 1.099339E+01 WEIGHT= 1.603600E-01 (electrostatic-local) ETURN3= 4.828306E+00 WEIGHT= 1.687220E+00 (turns, 3rd order) ETURN4= 7.195922E+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= -5.500000E+00 (disulfide-bridge intrinsic energy) UCONST= 0.000000E+00 (Constraint energy) ETOT= 4.145554E-01 (total) Initial: Kinetic energy 3.03426E+01 potential energy 4.14555E-01 total energy 3.07572E+01 maximum acceleration 6.47995E+01 dyn_ssbond_ene -4.98948276413721 dyn_ssbond_ene -4.98567582657971 dyn_ssbond_ene -4.98181834984520 dyn_ssbond_ene -4.97790946346179 dyn_ssbond_ene -4.97394802966017 dyn_ssbond_ene -4.96993269756970 dyn_ssbond_ene -4.96586197637466 dyn_ssbond_ene -4.96790432746792 dyn_ssbond_ene -4.96380533800446 dyn_ssbond_ene -4.96586191719089 dyn_ssbond_ene -4.96173426730095 dyn_ssbond_ene -4.95754722146956 dyn_ssbond_ene -4.95329741194513 dyn_ssbond_ene -4.94898099620549 dyn_ssbond_ene -4.94459341854952 dyn_ssbond_ene -4.94012975855659 dyn_ssbond_ene -4.94237113290313 dyn_ssbond_ene -4.93786820453041 dyn_ssbond_ene -4.94012941544864 dyn_ssbond_ene -4.93558597884915 dyn_ssbond_ene -4.93095640156330 dyn_ssbond_ene -4.92623208959982 dyn_ssbond_ene -4.92140234859462 dyn_ssbond_ene -4.91645468873417 dyn_ssbond_ene -4.91137490403000 dyn_ssbond_ene -4.90614681003041 dyn_ssbond_ene -4.90074757414400 dyn_ssbond_ene -4.89514182264486 dyn_ssbond_ene -4.90005816816882 dyn_ssbond_ene -4.89442278357481 dyn_ssbond_ene -4.89936543006444 dyn_ssbond_ene -4.89369806579643 dyn_ssbond_ene -4.89866921261761 dyn_ssbond_ene -4.89296196565191 dyn_ssbond_ene -4.89831967433662 dyn_ssbond_ene -4.89256930547234 dyn_ssbond_ene -4.89548166421252 dyn_ssbond_ene -4.88957751657537 dyn_ssbond_ene -4.89256772411923 dyn_ssbond_ene -4.88650680628924 dyn_ssbond_ene -4.88957623630728 dyn_ssbond_ene -4.88335595221106 dyn_ssbond_ene -4.88650579701510 dyn_ssbond_ene -4.88012413300318 dyn_ssbond_ene -4.88335526757055 dyn_ssbond_ene -4.87681094592356 dyn_ssbond_ene -4.88012384250956 dyn_ssbond_ene -4.87341651673553 dyn_ssbond_ene -4.87681113727144 dyn_ssbond_ene -4.86994163730936 dyn_ssbond_ene -4.87341729907754 dyn_ssbond_ene -4.86638793081870 dyn_ssbond_ene -4.86994314368993 dyn_ssbond_ene -4.86275804071596 dyn_ssbond_ene -4.86639031840578 dyn_ssbond_ene -4.85905583981676 dyn_ssbond_ene -4.86276148928941 dyn_ssbond_ene -4.85528663431195 dyn_ssbond_ene -4.86092008121014 dyn_ssbond_ene -4.85337924439134 dyn_ssbond_ene -4.85906125969940 dyn_ssbond_ene -4.85145783677887 dyn_ssbond_ene -4.85718573312957 dyn_ssbond_ene -4.84952353180303 dyn_ssbond_ene -4.85529430757408 dyn_ssbond_ene -4.84757754750072 dyn_ssbond_ene 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-0.223749865443158 dyn_ssbond_ene -0.210668030339004 dyn_ssbond_ene -0.217106315599577 dyn_ssbond_ene -0.204433617464602 dyn_ssbond_ene -0.210669527068736 dyn_ssbond_ene -0.198398020786750 dyn_ssbond_ene -0.204435385572321 dyn_ssbond_ene -0.192557675646151 dyn_ssbond_ene -0.198400066142955 dyn_ssbond_ene -0.186909125278448 dyn_ssbond_ene -0.192559958508285 dyn_ssbond_ene -0.181449044979786 dyn_ssbond_ene -0.186911614643331 dyn_ssbond_ene -0.176174171305381 dyn_ssbond_ene -0.181451698271930 dyn_ssbond_ene -0.171081264929712 dyn_ssbond_ene -0.176176939161129 dyn_ssbond_ene -0.166167049462255 dyn_ssbond_ene -0.171084083951287 =================================== Timing =================================== MD calculations setup: 5.07812E-02 Energy & gradient evaluation: 2.58203E+00 Stochastic MD setup: 0.00000E+00 Stochastic MD step setup: 0.00000E+00 MD steps: 1.84102E+02 ============================ End of MD calculation =========================== CG processor 0 is finishing work. Total wall clock time 184.757812500000 sec