[gmx-users] Gromacs Error

[Tsjerk Wassenaar]

Hi Manoj,

The error is clear. Check the settings referred to in your .mdp file and
modify them accordingly.

Cheers,

Tsjerk
On May 19, 2015 07:35, "manoj damale" <manojaurangabadkar at yahoo.co.in>
wrote:

> Dear All,
> i'm geting below error while subjecting my system (Protein-ligand) for
> equlibriation in nvt.mdp file
>
> mgmibt at mgmibt:~/gromacs-4.5.3/recent/files$ grompp -f nvt.mdp -c em.gro
> -p topol.top -n index.ndx -o nvt.tpr
>                          :-)  G  R  O  M  A  C  S  (-:
>
>                        GRowing Old MAkes el Chrono Sweat
>
>                             :-)  VERSION 4.5.3  (-:
>
>         Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>       Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
>         Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
>            Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
>                 Michael Shirts, Alfons Sijbers, Peter Tieleman,
>
>                Berk Hess, David van der Spoel, and Erik Lindahl.
>
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>             Copyright (c) 2001-2010, The GROMACS development team at
>         Uppsala University & The Royal Institute of Technology, Sweden.
>             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  (-:
>
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f        nvt.mdp  Input        grompp input file with MD parameters
>  -po      mdout.mdp  Output       grompp input file with MD parameters
>   -c         em.gro  Input        Structure file: gro g96 pdb tpr etc.
>   -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
>  -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
>   -n      index.ndx  Input, Opt!  Index file
>   -p      topol.top  Input        Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o        nvt.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
>
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -[no]version bool   no      Print version info and quit
> -nice        int    0       Set the nicelevel
> -[no]v       bool   no      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'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.18#
>
> ERROR 1 [file nvt.mdp]:
>   With coulombtype = PME-Switch, rcoulomb must be <= rlist
>
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'UNT'
> 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...
> Setting gen_seed to 3507
> Velocities were taken from a Maxwell distribution at 300 K
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.3
> Source code file: grompp.c, line: 1356
>
> Fatal error:
> There was 1 error in input file(s)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "Yeah, a Wuzz, Or a Jerk" (F. Black)
>  With Best Regards.
>
> Mr.Manoj Damale,
> M.S. Pharma (Pharmacoinformatics) NIPER,
> Kolkata, West Bengal State,
> India.
> --
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