-------------------------------------------------------------------------------- FILE ASSIGNMENT -------------------------------------------------------------------------------- Input file : 1L2Y_MD.inp Output file : 1L2Y_MD.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: 0.20000 natural units 9.78000 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: 10.00000 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 Langevin dynamics calculation with direct integration of Langevin equations Temperature: 300.00000 Viscosity of the solvent: 0.89040 Radius of solvent molecule: 1.40000 Scaling factor of the friction forces: 0.02000 Eta of the solvent in natural units: 49.27846 Radii of site types and friction coefficients and std's of stochastic forces of fully exposed sites p 2.50 3.84372 4.78549 CYS 5.00 6.30764 6.13033 MET 6.20 7.49033 6.68037 PHE 6.80 8.08167 6.93906 ILE 6.20 7.49033 6.68037 LEU 6.30 7.58888 6.72418 VAL 5.80 7.09610 6.50220 TRP 7.20 8.47589 7.10629 TYR 6.90 8.18022 6.98124 ALA 4.60 5.91342 5.93567 GLY 3.80 5.12496 5.52580 THR 5.60 6.89898 6.41125 SER 4.80 6.11053 6.03378 GLN 6.10 7.39177 6.63628 ASN 5.70 6.99754 6.45688 GLU 6.10 7.39177 6.63628 ASP 5.60 6.89898 6.41125 HIS 6.20 7.49033 6.68037 ARG 6.80 8.08167 6.93906 LYS 6.30 7.58888 6.72418 PRO 5.60 6.89898 6.41125 ============================== 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 Extended chain initial geometry. 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 1.684 110.000 -120.000 LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000 TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000 ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000 GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000 TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000 LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000 LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000 ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000 GLY 11 3.800 90.000 180.000 0.000 110.000 -120.000 GLY 12 3.800 90.000 180.000 0.000 110.000 -120.000 PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000 SER 14 3.800 90.000 180.000 1.150 110.000 -120.000 SER 15 3.800 90.000 180.000 1.150 110.000 -120.000 GLY 16 3.800 90.000 180.000 0.000 110.000 -120.000 ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000 PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000 PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000 PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000 SER 21 3.800 90.000 180.000 1.150 110.000 -120.000 D 22 3.800 90.000 180.000 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: 1.837610523517500E-017 -2.960594732333751E-018 9.596410511702503E-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 3.64779 0.96674 1.37044 LEU( 3) 3.80000 -3.80000 0.00000 2.68687 -3.62474 -1.57795 TYR( 4) 7.60000 -3.80000 0.00000 7.37548 -2.37399 2.02147 ILE( 5) 7.60000 -7.60000 0.00000 6.58044 -7.43947 -1.44530 GLN( 6) 11.40000 -7.60000 0.00000 11.19753 -6.31407 1.82291 TRP( 7) 11.40000 -11.40000 0.00000 9.90453 -11.16454 -2.11994 LEU( 8) 15.20000 -11.40000 0.00000 15.02474 -10.28687 1.57795 LYS( 9) 15.20000 -15.20000 0.00000 13.74127 -14.97033 -2.06786 ASP( 10) 19.00000 -15.20000 0.00000 18.84553 -14.21890 1.39078 GLY( 11) 19.00000 -19.00000 0.00000 19.00000 -19.00000 0.00000 GLY( 12) 22.80000 -19.00000 0.00000 22.80000 -19.00000 0.00000 PRO( 13) 22.80000 -22.80000 0.00000 22.02787 -22.67843 -1.09456 SER( 14) 26.60000 -22.80000 0.00000 26.49606 -22.13981 0.93587 SER( 15) 26.60000 -26.60000 0.00000 25.93981 -26.49606 -0.93587 GLY( 16) 30.40000 -26.60000 0.00000 30.40000 -26.60000 0.00000 ARG( 17) 30.40000 -30.40000 0.00000 28.66629 -30.12703 -2.45767 PRO( 18) 34.20000 -30.40000 0.00000 34.07843 -29.62787 1.09456 PRO( 19) 34.20000 -34.20000 0.00000 33.42787 -34.07843 -1.09456 PRO( 20) 38.00000 -34.20000 0.00000 37.87843 -33.42787 1.09456 SER( 21) 38.00000 -38.00000 0.00000 37.33981 -37.89606 -0.93587 D ( 22) 41.80000 -38.00000 0.00000 41.80000 -38.00000 0.00000 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 1.684 110.000 -120.000 LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000 TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000 ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000 GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000 TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000 LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000 LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000 ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000 GLY 11 3.800 90.000 180.000 0.000 180.000 180.000 GLY 12 3.800 90.000 180.000 0.000 180.000 180.000 PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000 SER 14 3.800 90.000 180.000 1.150 110.000 -120.000 SER 15 3.800 90.000 180.000 1.150 110.000 -120.000 GLY 16 3.800 90.000 180.000 0.000 180.000 180.000 ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000 PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000 PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000 PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000 SER 21 3.800 90.000 180.000 1.150 110.000 -120.000 D 22 3.800 90.000 180.000 0.000 180.000 180.000 Potential energy and its components Virtual-chain energies: EVDW= -1.947821E+01 WEIGHT= 1.000000D+00 (SC-SC) EVDW2= 2.387106E+01 WEIGHT= 1.233150D+00 (SC-p) EES= -7.520330E+00 WEIGHT= 8.447600D-01 (p-p) EVDWPP= -2.624923E+01 WEIGHT= 2.317300D-01 (p-p VDW) ESTR= 1.118676E+02 WEIGHT= 1.000000D+00 (stretching) EBE= -1.933948E+01 WEIGHT= 6.295400D-01 (bending) ESC= 8.868295E+01 WEIGHT= 1.055400D-01 (SC local) ETORS= 2.664535E-15 WEIGHT= 1.843160D+00 (torsional) ETORSD= -2.547586E+00 WEIGHT= 1.265710D+00 (double torsional) EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) ECORR4= -4.501075E+00 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= 2.197932E+01 WEIGHT= 3.735700D-01 (electrostatic-local) ETURN3= -1.258124E+00 WEIGHT= 1.403230D+00 (turns, 3rd order) ETURN4= 9.498513E+00 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= 1.150741E+02 (total) Initial: Kinetic energy 3.16218E+01 potential energy 1.15074E+02 total energy 1.46696E+02 maximum acceleration 4.85027E+00 =================================== Timing =================================== MD calculations setup: 7.81250E-03 Energy & gradient evaluation: 3.78934E+02 Stochastic MD setup: 0.00000E+00 Stochastic MD step setup: 0.00000E+00 MD steps: 4.56156E+02 ============================ End of MD calculation =========================== CG processor 0 is finishing work. Total wall clock time 456.886718750000 sec