[gmx-users] grompp warning
Mark.Abraham at anu.edu.au
Fri May 29 10:00:58 CEST 2009
sarbani chattopadhyay wrote:
> I have a 13 residue peptide which I have kept in a box using the
> following command
> editconf -f conf.gro -bt cubic -o box.gro -d 0.75
> the flag "-d 0.75" is given as per the ' minimum image convention'.
> When I solvate the box, 6772 water molecules get added.
> With such large no. of water molecules i get the following warning while
> using the "grompp"
> T coupling group is less than 10% of the total system.
So you're being warned that you may be doing something unsound. You're
actually probably OK - the warning is designed to alert newbies who are
(e.g.) erroneously T-coupling their three counter-ions separately.
> I have coupled the protein and solvent to the heat bath separately,
> using the terms
> "protein " and "non-protein".
> Moreover with such large no. of water molecules , the no.of degrees of
> freedom increases
> very much, and while doing Replica exchange md, I need to have more
> no.of replicas to
> maintain my desired acceptance ratio.
> How can I avoid this problem?
That's a cost of doing business. There are a variety of approximations
to REMD that are designed to get around this issue, but none are
implemented in GROMACS, to my knowledge.
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