[gmx-users] simulation broke at 4.0.5 version
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Jan 7 08:10:57 CET 2010
Chih-Ying Lin wrote:
>
> Hi
> I am using Gromacs version 4.0.5.
> I put one protein in a simulation box with water molecules and CL- only.
> My simulation broke at the step, Relaxation of solvent and hydrogen atom
> position.
> Here are the .top file, command, output of the grommp, pr.mdp.
>
>
> anything wrong here?
Not obviously. Depending what you mean by "broke", your starting
configuration is probably broken, or you've mismatched input files in
some way.
Mark
> Thank you
> Lin
>
>
>
>
> *[6YZ.top]*
>
> [ molecules ]
> ; Compound #mols
> Protein_A 1
> SOL 6504
> CL- 8
>
>
>
>
> *Relaxation of solvent and hydrogen atom positions: Position restrained MD*
>
> *[command]*
>
> grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr
>
>
>
> mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR
>
>
>
>
>
>
>
> *[output of the grompp comand]*
> 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 (-:
> Gyas ROwers Mature At Cryogenic Speed
> :-) 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 <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.1#
> 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/ffG45a3.itp
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG45a3nb.itp
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG45a3bon.itp
> Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ff_dum.itp
> Generated 141 of the 1176 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#264: "RTFM" (B. Hess)
>
>
>
> *[pr.mdp]*
> **
> ; VARIOUS PREPROCESSING OPTIONS
> title =
> cpp = /lib/cpp
> include =
> define = -DPOSRES
> ; RUN CONTROL PARAMETERS
> integrator = md
> tinit = 0
> dt = 0.001
> nsteps = 5000
> nstcomm = 0
> ; OUTPUT CONTROL OPTIONS
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstlog = 10
> nstenergy = 1
> nstxtcout = 0
> xtc_precision = 1000
> xtc-grps = System
> energygrps = Protein Non-Protein
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist = 5
> ns-type = Grid
> pbc = xyz
> rlist = 0.9
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype = Reaction-Field
> rcoulomb = 1.4
> epsilon_rf = 78
> epsilon_r = 1
> vdw-type = Cut-off
> rvdw = 1.4
> ; Temperature coupling
> Tcoupl = Berendsen
> tc-grps = Protein Non-Protein
> tau_t = 0.1 0.1
> ref_t = 200 200
> ; Pressure coupling
> Pcoupl = No
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel = yes
> gen_temp = 200.0
> gen_seed = 1735
> ; OPTIONS FOR BONDS
> constraints = all-bonds
> constraint-algorithm = Lincs
> unconstrained-start = no
> lincs-order = 4
> lincs-iter = 1
> lincs-warnangle = 30
>
>
>
>
>
>
More information about the gromacs.org_gmx-users
mailing list