+++ /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
projects / unres.git / blobdiff