[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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