[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken (output file)

Itamar Kass itamar.kass at gmail.com
Sun Jan 10 04:09:05 CET 2010


Hi,

It is not clear to me if you did EM or not. If you didn't, it is highly
advisable to do short EM before you start your PR step.

Best,
Itamar

On Sun, Jan 10, 2010 at 1:29 PM, Chih-Ying Lin <chihying2008 at gmail.com>wrote:

>
> Hi
> 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running
> the simulation on Gromacs.
> System = 6LYZ.pdb + CL- + water molecules
>
> Before I put the 6LYZ.pdb on Gromacs 3.3.3, there is no problem at all.
> Recently, I tried the Gromacs 4.0.5, the simulation is broken at the step
> Position restrained MD.
>
> The commands are as follows.
> minim.mdp and pr.mdp are as follows.
> And outputs are as follows.
>
> Any thing wrong?
> Thank you
> Lin
>
>
>
> =======================================================================================================
>
> - Hide quoted text -
> grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o
> 6LYZ-EM-solvated
>                          :-)  G  R  O  M  A  C  S  (-:
>                    Good gRace! Old Maple Actually Chews Slate
>                             :-)  VERSION 4.0.5  (-:
>       Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>              Copyright (c) 2001-2008, The GROMACS development team,
>             check out http://www.gromacs.org for more information.
>          This program is free software; you can redistribute it and/or
>           modify it under the terms of the GNU General Public License
>          as published by the Free Software Foundation; either version 2
>              of the License, or (at your option) any later version.
>                               :-)  grompp_mpi  (-:
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f      minim.mdp  Input, Opt!  grompp input file with MD parameters
>  -po      mdout.mdp  Output       grompp input file with MD parameters
>   -c 6LYZ-solvated.gro  Input        Structure file: gro g96 pdb tpr tpb
> tpa
>   -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>  -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>   -n      index.ndx  Input, Opt.  Index file
>   -p       6LYZ.top  Input        Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o 6LYZ-EM-solvated.tpr  Output       Run input file: tpr tpb tpa
>   -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
>   -e       ener.edr  Input, Opt.  Energy file: edr ene
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -nice        int    0       Set the nicelevel
> -[no]v       bool   yes     Be loud and noisy
> -time        real   -1      Take frame at or first after this time.
> -[no]rmvsbds bool   yes     Remove constant bonded interactions with
> virtual
>                             sites
> -maxwarn     int    0       Number of allowed warnings during input
> processing
> -[no]zero    bool   no      Set parameters for bonded interactions without
>                             defaults to zero instead of generating an error
> -[no]renum   bool   yes     Renumber atomtypes and minimize number of
>                             atomtypes
> Ignoring obsolete mdp entry 'title'
> Ignoring obsolete mdp entry 'cpp'
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> processing topology...
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2.itp
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2nb.itp
> Opening library file
> /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2bon.itp
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ff_dum.itp
> Generated 380 of the 1326 non-bonded parameter combinations
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Excluding 1 bonded neighbours molecule type 'CL-'
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> initialising group options...
> processing index file...
> Analysing residue names:
> Opening library file
> /usr/usc/gromacs/4.0.5/share/gromacs/top/aminoacids.dat
> There are:  6512      OTHER residues
> There are:   129    PROTEIN residues
> There are:     0        DNA residues
> Analysing Protein...
> Analysing Other...
> Making dummy/rest group for T-Coupling containing 20841 elements
> Making dummy/rest group for Acceleration containing 20841 elements
> Making dummy/rest group for Freeze containing 20841 elements
> Making dummy/rest group for VCM containing 20841 elements
> Number of degrees of freedom in T-Coupling group rest is 62520.00
> Making dummy/rest group for User1 containing 20841 elements
> Making dummy/rest group for User2 containing 20841 elements
> Making dummy/rest group for XTC containing 20841 elements
> Making dummy/rest group for Or. Res. Fit containing 20841 elements
> Making dummy/rest group for QMMM containing 20841 elements
> T-Coupling       has 1 element(s): rest
> Energy Mon.      has 1 element(s): System
> Acceleration     has 1 element(s): rest
> Freeze           has 1 element(s): rest
> User1            has 1 element(s): rest
> User2            has 1 element(s): rest
> VCM              has 1 element(s): rest
> XTC              has 1 element(s): rest
> Or. Res. Fit     has 1 element(s): rest
> QMMM             has 1 element(s): rest
> Checking consistency between energy and charge groups...
> NOTE 1 [file minim.mdp, line unknown]:
>   You are using a plain Coulomb cut-off, which might produce artifacts.
>   You might want to consider using PME electrostatics.
> This run will generate roughly 242 Mb of data
> writing run input file...
> There was 1 note
> Back Off! I just backed up 6LYZ-EM-solvated.tpr to
> ./#6LYZ-EM-solvated.tpr.1#
> gcq#13: "If Life Seems Jolly Rotten, There's Something You've Forgotten !"
> (Monty Python)
>
>
>
>
> =================================================================================================================
>
>  grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr
>
>                          :-)  G  R  O  M  A  C  S  (-:
>                Giant Rising Ordinary Mutants for A Clerical Setup
>                             :-)  VERSION 4.0.5  (-:
>       Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>              Copyright (c) 2001-2008, The GROMACS development team,
>             check out http://www.gromacs.org for more information.
>          This program is free software; you can redistribute it and/or
>           modify it under the terms of the GNU General Public License
>          as published by the Free Software Foundation; either version 2
>              of the License, or (at your option) any later version.
>                               :-)  grompp_mpi  (-:
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f         pr.mdp  Input, Opt!  grompp input file with MD parameters
>  -po      mdout.mdp  Output       grompp input file with MD parameters
>   -c 6LYZ-EM-solvated.gro  Input        Structure file: gro g96 pdb tpr tpb
>                                    tpa
>   -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>  -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>   -n      index.ndx  Input, Opt.  Index file
>   -p       6LYZ.top  Input        Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o    6LYZ-PR.tpr  Output       Run input file: tpr tpb tpa
>   -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
>   -e       ener.edr  Input, Opt.  Energy file: edr ene
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -nice        int    0       Set the nicelevel
> -[no]v       bool   yes     Be loud and noisy
> -time        real   -1      Take frame at or first after this time.
> -[no]rmvsbds bool   yes     Remove constant bonded interactions with
> virtual
>                             sites
> -maxwarn     int    0       Number of allowed warnings during input
> processing
> -[no]zero    bool   no      Set parameters for bonded interactions without
>                             defaults to zero instead of generating an error
> -[no]renum   bool   yes     Renumber atomtypes and minimize number of
>                             atomtypes
> Ignoring obsolete mdp entry 'cpp'
> Replacing old mdp entry 'unconstrained-start' by 'continuation'
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
> checking input for internal consistency...
> NOTE 1 [file pr.mdp, line unknown]:
>   The Berendsen thermostat does not generate the correct kinetic energy
>   distribution. You might want to consider using the V-rescale thermostat.
> processing topology...
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2.itp
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2nb.itp
> Opening library file
> /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2bon.itp
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ff_dum.itp
> Generated 380 of the 1326 non-bonded parameter combinations
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'CL-'
> turning all bonds into constraints...
> processing coordinates...
> double-checking input for internal consistency...
> Velocities were taken from a Maxwell distribution at 200 K
> Reading position restraint coords from 6LYZ-EM-solvated.gro
> renumbering atomtypes...
> converting bonded parameters...
> initialising group options...
> processing index file...
> Analysing residue names:
> Opening library file
> /usr/usc/gromacs/4.0.5/share/gromacs/top/aminoacids.dat
> There are:  6512      OTHER residues
> There are:   129    PROTEIN residues
> There are:     0        DNA residues
> Analysing Protein...
> Analysing Other...
> Making dummy/rest group for Acceleration containing 20841 elements
> Making dummy/rest group for Freeze containing 20841 elements
> Making dummy/rest group for VCM containing 20841 elements
> Number of degrees of freedom in T-Coupling group Protein is 2618.00
> Number of degrees of freedom in T-Coupling group Non-Protein is 39048.00
> Making dummy/rest group for User1 containing 20841 elements
> Making dummy/rest group for User2 containing 20841 elements
> Making dummy/rest group for Or. Res. Fit containing 20841 elements
> Making dummy/rest group for QMMM containing 20841 elements
> T-Coupling       has 2 element(s): Protein Non-Protein
> Energy Mon.      has 2 element(s): Protein Non-Protein
> Acceleration     has 1 element(s): rest
> Freeze           has 1 element(s): rest
> User1            has 1 element(s): rest
> User2            has 1 element(s): rest
> VCM              has 1 element(s): rest
> XTC              has 1 element(s): System
> Or. Res. Fit     has 1 element(s): rest
> QMMM             has 1 element(s): rest
> Checking consistency between energy and charge groups...
> This run will generate roughly 3 Mb of data
> writing run input file...
> There was 1 note
> Back Off! I just backed up 6LYZ-PR.tpr to ./#6LYZ-PR.tpr.1#
> gcq#52: "I'm a Wishbone and I'm Breaking" (Pixies)
>
>
>
>
> ====================================================================================================
>
>
>
>
> ======================================================================================================
> .out file
>
>
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    1005   1006   41.4    0.1625   0.1078      0.1430
>    1006   1007   30.6    0.1044   0.0899      0.1000
>    1077   1081  129.5    0.2893   0.5930      0.1390
>    1077   1078  102.3    0.0542   1.1847      0.1090
>    1073   1077  167.5    1.0876   0.9651      0.1390
>    1073   1076   57.2    0.6969   1.7573      0.1390
>    1074   1076   63.8    0.6555   1.2119      0.1330
>    1074   1075  101.0    1.3130   1.1709      0.1000
>    1071   1074  108.5    1.0586   0.4070      0.1330
>    1071   1072   94.2    0.6662   1.3755      0.1090
>    1070   1071  114.1    0.6490   0.6753      0.1330
>    1070   1073  155.5    1.0880   1.0783      0.1390
>    1069   1070   78.1    0.2488   1.2798      0.1530
>
>
>
>
>
>
> --
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