[gmx-users] Problem in NVT equilibration

[Balasubramanian Suriyanarayanan]

Sir, Thanks for your reply.

I really works. But the next error message was "Group SOL_CL not found in
indexfile.
Maybe you have non-default goups in your .mdp file, while not using the
'-n' option of grompp.
In that case use the '-n' option"

 But I have really used "-n" option.


regards

Suriyanarayanan



On Mon, Jun 9, 2014 at 3:00 PM, Venkat Reddy <venkat4bt at gmail.com> wrote:

> Dear Surinarayanan,
> You have to create appropriate index file by grouping solvent and solute
> molecules separately (eg: Protein_ligand_membrane      Water_and_ions).
>
>
> On Mon, Jun 9, 2014 at 12:33 PM, Balasubramanian Suriyanarayanan <
> bsnsuri at gmail.com> wrote:
>
> > Dear User
> >  I do a protein ligand simulation in a lipid environment.  When I do NVT
> > equilibration I get an error message saying "32 molecules are not part of
> > any coupling groups".
> >
> > Do I need to change the .mdp file.
> >
> > Please clarify.
> >
> > Regards
> >
> > Surinarayanan
> > --
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>
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
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