[gmx-users] Re: a question about gromacs-water tutorial

Justin A. Lemkul jalemkul at vt.edu
Mon Jan 4 13:19:11 CET 2010

Please keep all Gromacs-related correspondence on the gmx-users list.  This has 
nothing to do with any of my tutorials, and as such, is better posted to the 
community.  As I seem to post every other day or so, I am not a private tutor or 
help service.

The grompp.mdp file in the /share/tutor subdirectory is outdated.  A quick look 
at the manual explains warning #1; this parameter does not exist.  The other two 
notes are clearly explained by grompp.  For the purposes of running through the 
example in /share/tutor, you can set -maxwarn 1 (which is not generally 
advisable, but in this case is OK), or modify the grompp.mdp file to contain 
relevant settings.


mohammad Kowsari wrote:
> Dear Justin,
> I mailed to you in the previous month about your gromacs tutorials.
> now, I start with gromacs tutor sub-directory in the share folder.
> for example, for both water and methanol example, when I run grompp -v
> , I see these problem message:
> WARNING 1 [file grompp.mdp, line unknown]:
>   Unknown or double left-hand 'bd-temp' in parameter file
> 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.
> NOTE 2 [file grompp.mdp, line unknown]:
>   You are using a plain Coulomb cut-off, which might produce artifacts.
>   You might want to consider using PME electrostatics.
> Program grompp, VERSION 4.0.5
> 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.
> -------------------------------------------------------
>  in these condition, gromacs generate "mdout.mdp" file but no generate
> "topol.tpr" file.
> when I used this options:        grompp -v -maxwarn 1
> the pre-processing is done and the topol.tpr file is constracted.
> Is it possible and correct to use of "-maxwarn 1" for run these
> tutorial example or not?!?
> Best Regards,
> M. H. Kowsari
> PhD of Physical Chemistry
> Isfahan University of Technology, 84156-83111
> Isfahan, IRAN


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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