--- /dev/null
+--------------------------------------------------------------------------------
+ FILE ASSIGNMENT
+--------------------------------------------------------------------------------
+ Input file : 1L2Y_MD.inp
+ Output file : 1L2Y_MD.out_GB000
+
+ Sidechain potential file :
+ /users/czarek/UNRES/export_v3/PARAM/scinter_GB.parm
+ SCp potential file : /users/czarek/UNRES/export_v3/PARAM/scp.parm
+ Electrostatic potential file :
+ /users/czarek/UNRES/export_v3/PARAM/electr_631Gdp.parm
+ Cumulant coefficient file :
+ /users/czarek/UNRES/export_v3/PARAM/fourier_opt.parm.1igd_hc_iter3_3
+ Torsional parameter file :
+ /users/czarek/UNRES/export_v3/PARAM/torsion_631Gdp.parm
+ Double torsional parameter file :
+ /users/czarek/UNRES/export_v3/PARAM/torsion_double_631Gdp.parm
+ SCCOR parameter file : /users/czarek/UNRES/export_v3/PARAM/rotcorr_AM1.parm
+ Bond & inertia constant file : /users/czarek/UNRES/export_v3/PARAM/bond.parm
+ Bending parameter file :
+ /users/czarek/UNRES/export_v3/PARAM/thetaml.5parm
+ Rotamer parameter file :
+ /users/czarek/UNRES/export_v3/PARAM/scgauss.parm
+ Threading database :
+ /users/czarek/UNRES/export_v3/PARAM/patterns.cart
+--------------------------------------------------------------------------------
+********************************************************************************
+United-residue force field calculation - parallel job.
+********************************************************************************
+ ### LAST MODIFIED 04/08/11 11:00AM by czarek
+ ++++ Compile info ++++
+ Version 2.5 build 36
+ compiled Thu Dec 1 05:12:23 2011
+ compiled by czarek@matrix.chem.cornell.edu
+ OS name: Linux
+ OS release: 2.6.34.8-68.fc13.x86_64
+ OS version: #1 SMP Thu Feb 17 15:03:58 UTC 2011
+ flags:
+ CPPFLAGS = -DCRYST_BOND -DCRYST_THETA -DCRYST_S...
+ 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 ...
+ BIN = ../bin/unres_120111_mpich1_oldparm.exe
+ LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr...
+ ARCH = LINUX
+ PP = /lib/cpp -P
+ object = unres.o arcos.o cartprint.o chainbuild...
+ ++++ 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= -3059742
+ ran_num 0.273754117333397
+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 5.00 6.30764 6.13033
+ 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= 1.352790 (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 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 0.14116 0.06019 0.00651 0.00000 0.00000 0.00000
+ 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
+ 2 -0.17175 -0.01249 -0.15331 -0.02090 -0.05792 -0.09881
+ 3 0.15276 0.01076 0.15619 -0.00869 -0.01649 0.14952
+ 4 0.09714 0.21962 -0.00076 -0.13161 0.00105 -0.13191
+ 5 -0.28995 -0.28661 -0.04399 -0.20794 -0.09712 0.06109
+ 6 0.02606 -0.09397 0.00121 0.02142 0.02371 0.06777
+ 7 0.14043 0.10719 0.11062 0.03017 0.12211 0.14888
+ 8 -0.15894 0.05289 -0.04945 -0.08870 -0.06076 0.05527
+ 9 0.00083 -0.06721 -0.12843 0.11538 -0.05179 -0.14286
+ 10 0.29223 -0.07835 0.13064 0.07317 0.00083 0.11341
+ 11 -0.41159 0.15104 -0.01780 0.00000 0.00000 0.00000
+ 12 0.28145 -0.01326 0.08243 0.00000 0.00000 0.00000
+ 13 -0.33623 0.09347 -0.10808 -0.02992 0.03048 -0.13246
+ 14 0.40983 0.00917 -0.03051 0.24109 -0.19177 -0.02812
+ 15 -0.14238 -0.04269 0.11329 -0.06397 -0.14551 -0.10490
+ 16 -0.11159 -0.01629 0.01549 0.00000 0.00000 0.00000
+ 17 0.08712 -0.04737 0.04618 0.02491 -0.13909 -0.04091
+ 18 -0.17195 -0.14441 -0.13341 0.13324 -0.01700 -0.06373
+ 19 0.13399 0.09745 -0.00585 0.01171 0.10181 -0.02391
+ 20 -0.08296 -0.16674 0.16475 0.07397 -0.09732 -0.22217
+ 21 0.00000 0.00000 0.00000 0.05726 0.10954 -0.06352
+ 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
+ Calling the zero-angular momentum subroutine
+ vcm right after adjustment:
+ 2.057102891604313E-017 3.164773679391251E-017 -5.308652623495002E-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= 1.352790D+00 (SC-SC)
+EVDW2= 2.387106E+01 WEIGHT= 1.593040D+00 (SC-p)
+EES= -7.520330E+00 WEIGHT= 7.153400D-01 (p-p)
+EVDWPP= -2.624923E+01 WEIGHT= 1.137100D-01 (p-p VDW)
+ESTR= 8.665144E-27 WEIGHT= 1.000000D+00 (stretching)
+EBE= 1.082023E+00 WEIGHT= 1.138730D+00 (bending)
+ESC= 9.168846E+01 WEIGHT= 1.625800D-01 (SC local)
+ETORS= 2.664535E-15 WEIGHT= 1.985990D+00 (torsional)
+ETORSD= -2.547586E+00 WEIGHT= 1.570690D+00 (double torsional)
+EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4= -4.501075E+00 WEIGHT= 4.288700D-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= 1.603600D-01 (electrostatic-local)
+ETURN3= -1.258124E+00 WEIGHT= 1.687220D+00 (turns, 3rd order)
+ETURN4= 9.498513E+00 WEIGHT= 6.623000D-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= 2.121298E+01 (total)
+
+Initial:
+ Kinetic energy 2.60624E+01
+ potential energy 2.12130E+01
+ total energy 4.72754E+01
+
+ maximum acceleration 9.35162E-01
+
+
+
+=================================== Timing ===================================
+
+ MD calculations setup: 7.81250E-03
+ Energy & gradient evaluation: 3.11953E+02
+ Stochastic MD setup: 0.00000E+00
+ Stochastic MD step setup: 0.00000E+00
+ MD steps: 3.65984E+02
+
+
+============================ End of MD calculation ===========================
+CG processor 0 is finishing work.
+ Total wall clock time 373.972656250000 sec