[gmx-users] grompp warning

sarbani chattopadhyay 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.

Thank You,
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