[gmx-users] Problem in NVT equilibration

[Venkat Reddy]

Hi,
No need to group SOL and ions. They will default present in index group as
Water_and_ions. Just mention Water_and_ions in your mdp file.


On Mon, Jun 9, 2014 at 5:26 PM, Balasubramanian Suriyanarayanan <
bsnsuri at gmail.com> wrote:

> 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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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036