[gmx-users] problem in running gromacs demo

[Mark Abraham]

nitu sharma wrote:
> Dear all,
> 
>                        I  have successfully installed the gromacs 4.0.3  
> it is working but the problem is when I want to run the gromacs demo 
> during processing when I put the command "grompp -v" the output like 
> this ,:-)  G  R  O  M  A  C  S  (-:
> 
>                   Gromacs Runs On Most of All Computer Systems
> 
>                             :-)  VERSION 4.0.3  (-:
> 
> 
>       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  (-:
> 
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f     grompp.mdp  Input, Opt.  grompp input file with MD parameters
>  -po      mdout.mdp  Output       grompp input file with MD parameters
>   -c       conf.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      topol.top  Input        Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o      topol.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'
> Ignoring obsolete mdp entry 'domain-decomposition'
> Replacing old mdp entry 'unconstrained-start' by 'continuation'
> Ignoring obsolete mdp entry 'dihre-tau'
> Ignoring obsolete mdp entry 'nstdihreout'
> Ignoring obsolete mdp entry 'nstcheckpoint'
> 
> WARNING 1 [file grompp.mdp, line unknown]:
>   Unknown or double left-hand 'bd-temp' in parameter file
> 
> 
> checking input for internal consistency...
> 
> NOTE 1 [file grompp.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/local/gromacs/share/gromacs/top/ffgmx.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxnb.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxbon.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
> Generated 1284 of the 1485 non-bonded parameter combinations
> Excluding 2 bonded neighbours molecule type 'SOL'
> processing coordinates...
> double-checking input for internal consistency...
> Velocities were taken from a Maxwell distribution at 300 K
> renumbering atomtypes...
> converting bonded parameters...
> initialising group options...
> processing index file...
> Analysing residue names:
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> There are:   216      OTHER residues
> There are:     0    PROTEIN residues
> There are:     0        DNA residues
> Analysing Other...
> Making dummy/rest group for Acceleration containing 648 elements
> Making dummy/rest group for Freeze containing 648 elements
> Making dummy/rest group for Energy Mon. containing 648 elements
> Making dummy/rest group for VCM containing 648 elements
> Number of degrees of freedom in T-Coupling group System is 1293.00
> Making dummy/rest group for User1 containing 648 elements
> Making dummy/rest group for User2 containing 648 elements
> Making dummy/rest group for XTC containing 648 elements
> Making dummy/rest group for Or. Res. Fit containing 648 elements
> Making dummy/rest group for QMMM containing 648 elements
> T-Coupling       has 1 element(s): System
> Energy Mon.      has 1 element(s): rest
> 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 2 [file grompp.mdp, line unknown]:
>   You are using a plain Coulomb cut-off, this will often produce artifacts.
>   You might want to consider using PME electrostatics.
> 
> 
> This run will generate roughly 1 Mb of data
> writing run input file...
> 
> There were 2 notes
> 
> There was 1 warning
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.0.3
> Source code file: gmx_fatal.c, line: 481
> 
> Fatal error:
> Too many warnings (1), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> -------------------------------------------------------
> 
> "How Do You Like Your Vacation So Far ?" (Speed 2 - Cruise Control) why 
> the grompp -v terminated  even i am going step by step as in mannual.
> could you please anybody tell me about that.
>  Thank you very much in advance.

The existence of this list doesn't mean you don't have to do your own 
detective work! Nobody's paying any of us to help anybody, and we'll be 
much more inclined to give our valuable time to you if you've 
demonstrated a genuine attempt to solve your own problem.

This error message is explicit. There's a fatal error because there's 
too many warnings. There's one warning given. Read it and draw your own 
conclusions :-)

Whatever demonstration you're doing was also probably written for a 
GROMACS version below 4, so you should expect some differences.

Mark