--- /dev/null
+--------------------------------------------------------------------------------
+ FILE ASSIGNMENT
+--------------------------------------------------------------------------------
+ Input file : 1L2Y_micro.inp
+ Output file : 1L2Y_micro.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: 0.01000 natural units
+ 0.48900 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: 20.00000
+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
+Microcanonical mode calculation
+
+============================== 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
+
+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 3.861 0.000 0.000 1.977 94.624 -178.093
+LEU 3 3.876 92.239 0.000 2.195 102.878 -79.236
+TYR 4 3.861 92.239 -180.000 3.330 163.195 -7.440
+ILE 5 3.871 90.357 45.849 1.692 144.011 -104.516
+GLN 6 3.846 89.090 55.194 2.338 170.986 -139.318
+TRP 7 3.867 88.657 49.396 3.617 123.650 -21.913
+LEU 8 3.859 93.032 48.298 2.105 151.723 -105.899
+LYS 9 3.882 94.826 46.843 2.997 106.974 -55.960
+ASP 10 3.861 87.966 59.623 1.991 153.447 -128.646
+GLY 11 3.891 89.908 56.679 0.000 0.000 0.000
+GLY 12 3.864 100.181 -87.304 0.000 0.000 0.000
+PRO 13 3.886 109.073 -127.499 1.402 101.771 -115.580
+SER 14 3.876 89.537 4.261 1.267 144.515 -129.218
+SER 15 3.875 91.815 66.108 1.262 161.047 -100.177
+GLY 16 3.866 101.784 70.140 0.000 0.000 0.000
+ARG 17 3.866 92.201 -108.949 3.411 139.846 -132.716
+PRO 18 3.878 133.225 103.824 1.397 115.610 -118.024
+PRO 19 3.860 121.502 -122.527 1.395 118.575 -122.417
+PRO 20 3.858 117.950 -90.285 1.396 118.959 -126.207
+SER 21 3.864 114.201 -108.328 0.708 128.925 -37.341
+D 22 3.858 114.201 180.000 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:
+ 4.226504204090251E-017 -1.020894735287500E-018 -4.083578941150001E-019
+
+
+ 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) 3.86050 0.00000 0.00000 2.55159 1.47985 0.06557
+LEU( 3) 4.01193 -3.87344 0.00000 3.96088 -4.50305 -2.10206
+TYR( 4) 7.87243 -3.87344 0.00000 10.79652 -4.89021 -1.22632
+ILE( 5) 7.89655 -1.17680 2.77774 7.76075 0.44675 2.31935
+GLN( 6) 5.70141 -3.47509 4.94285 3.60888 -3.02771 5.88565
+TRP( 7) 8.16996 -6.36206 4.22016 10.77228 -8.29798 2.61912
+LEU( 8) 11.25658 -4.20989 5.07405 12.42370 -3.38205 3.52958
+LYS( 9) 9.76612 -2.79308 8.36640 6.86736 -2.82804 9.12493
+ASP( 10) 9.49962 -6.42561 9.64741 7.69328 -7.25489 9.53489
+GLY( 11) 13.31647 -6.90493 9.06335 13.31647 -6.90493 9.06335
+GLY( 12) 13.30671 -8.01769 5.36352 13.30671 -8.01769 5.36352
+PRO( 13) 15.31165 -11.32992 5.02827 16.17763 -10.48298 4.32295
+SER( 14) 15.75414 -11.41497 8.87760 16.77305 -10.71800 9.16233
+SER( 15) 11.95328 -11.92981 9.42670 11.12717 -10.97987 9.51528
+GLY( 16) 11.45094 -15.53878 8.13618 11.45094 -15.53878 8.13618
+ARG( 17) 9.54906 -14.31220 5.00147 7.79760 -12.40573 7.22288
+PRO( 18) 10.53690 -13.94710 1.26956 9.62009 -14.99504 1.15440
+PRO( 19) 10.30439 -10.55356 -0.55592 11.52337 -10.99526 -1.06954
+PRO( 20) 6.99735 -9.68439 -2.34313 7.03150 -8.66136 -1.39345
+SER( 21) 7.20688 -9.78655 -6.20031 7.28380 -10.16020 -6.79638
+D ( 22) 3.89984 -8.91739 -7.98752 3.89984 -8.91739 -7.98752
+
+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 3.861 0.000 0.000 1.977 94.624 -178.093
+LEU 3 3.876 92.239 0.000 2.195 102.878 -79.236
+TYR 4 3.861 92.239 -180.000 3.330 163.195 -7.440
+ILE 5 3.871 90.357 45.849 1.692 144.011 -104.516
+GLN 6 3.846 89.090 55.194 2.338 170.986 -139.318
+TRP 7 3.867 88.657 49.396 3.617 123.650 -21.913
+LEU 8 3.859 93.032 48.298 2.105 151.723 -105.899
+LYS 9 3.882 94.826 46.843 2.997 106.974 -55.960
+ASP 10 3.861 87.966 59.623 1.991 153.447 -128.646
+GLY 11 3.891 89.908 56.679 0.000 180.000 180.000
+GLY 12 3.864 100.181 -87.304 0.000 180.000 180.000
+PRO 13 3.886 109.073 -127.499 1.402 101.771 -115.580
+SER 14 3.876 89.537 4.261 1.267 144.515 -129.218
+SER 15 3.875 91.815 66.108 1.262 161.047 -100.177
+GLY 16 3.866 101.784 70.140 0.000 180.000 180.000
+ARG 17 3.866 92.201 -108.949 3.411 139.846 -132.716
+PRO 18 3.878 133.225 103.824 1.397 115.610 -118.024
+PRO 19 3.860 121.502 -122.527 1.395 118.575 -122.417
+PRO 20 3.858 117.950 -90.285 1.396 118.959 -126.207
+SER 21 3.864 114.201 -108.328 0.708 128.925 -37.341
+D 22 3.858 114.201 180.000 0.000 180.000 180.000
+ Potential energy and its components
+
+Virtual-chain energies:
+
+EVDW= -1.798849E+01 WEIGHT= 1.000000D+00 (SC-SC)
+EVDW2= 4.471415E+01 WEIGHT= 1.233150D+00 (SC-p)
+EES= -9.165378E+01 WEIGHT= 8.447600D-01 (p-p)
+EVDWPP= -3.362882E+01 WEIGHT= 2.317300D-01 (p-p VDW)
+ESTR= 5.659036E+01 WEIGHT= 1.000000D+00 (stretching)
+EBE= -5.669935E+00 WEIGHT= 6.295400D-01 (bending)
+ESC= 1.734458E+02 WEIGHT= 1.055400D-01 (SC local)
+ETORS= 1.479510E+01 WEIGHT= 1.843160D+00 (torsional)
+ETORSD= 1.006444E+00 WEIGHT= 1.265710D+00 (double torsional)
+EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4= -6.528803E+01 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= -4.012900E+00 WEIGHT= 3.735700D-01 (electrostatic-local)
+ETURN3= 1.829789E+01 WEIGHT= 1.403230D+00 (turns, 3rd order)
+ETURN4= 6.580750E-01 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= 6.386200E+01 (total)
+
+Initial:
+ Kinetic energy 3.07644E+01
+ potential energy 6.38620E+01
+ total energy 9.46264E+01
+
+ maximum acceleration 1.97191E+00
+
+ acceleration/energy drift too large 24.8795828613454
+ 0.393622871058234 split increased to 2 itime 49077
+ itsplit 1
+
+
+=================================== Timing ===================================
+
+ MD calculations setup: 3.90625E-03
+ Energy & gradient evaluation: 3.56734E+02
+ Stochastic MD setup: 0.00000E+00
+ Stochastic MD step setup: 0.00000E+00
+ MD steps: 3.91938E+02
+
+
+============================ End of MD calculation ===========================
+CG processor 0 is finishing work.
+ Total wall clock time 401.093750000000 sec
projects / unres.git / blobdiff