[gmx-users] MD simulations

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jul 30 12:52:53 CEST 2015

Hi :)

The error is that there are warnings. Well, one warning. A warning from
grompp may indicate an inconsistency in the topology (like atom name
mismatch), an incompatibility of MDP parameters which grompp corrects
automatically (nst*), or a possible pitfall (like too many temperature
coupling groups or so). These are things that a user may intend or allow,
so they are not directly raising an error, but generate warnings. One can
specify the number of warnings allowed, based on the number expected or
previously observed. However, warnings should never be neglected without
thinking about them. The warnings are marked with "WARNING" in the grompp
output. Under normal circumstances, normal users doing normal (atomistic)
simulations should not encounter warnings.

Hope it helps,


On Thu, Jul 30, 2015 at 11:42 AM, soumadwip ghosh <soumadwipghosh at gmail.com>

> What is the error displayed when you run grompp? Is it related to the
> topology mismatch, wrong mdp parameters, domain decomposition error,
> shake/Lincs error or something else? There are so many possibilities and
> unless you write the exact error statement issued by grompp it is
> impossible for anyone to help you.
> Soumadwip
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Tsjerk A. Wassenaar, Ph.D.

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