-------------------------------------------------------------------------------- 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: 0.10000 natural units 4.89000 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 Nose-Hoover bath calculation Mol.Phys. 87 1117 (1996) Martyna et al. NVT-XI-RESPA algorithm Temperature: 300.00000 Q = 1.00000 ============================== 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 H0= 212.829722601506 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: 4.68750E-02 Energy & gradient evaluation: 3.77336E+02 Stochastic MD setup: 0.00000E+00 Stochastic MD step setup: 0.00000E+00 MD steps: 4.15750E+02 ============================ End of MD calculation =========================== CG processor 0 is finishing work. Total wall clock time 420.417968750000 sec