--- /dev/null
+--------------------------------------------------------------------------------
+ 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
projects / unres.git / blobdiff