[gmx-users] grompp warning
sarbani_c84 at rediffmail.com
Fri May 29 09:42:52 CEST 2009
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.
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?
Any suggestion will be very helpful.
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