[gmx-users] nvt T coupling group problem

rajat desikan rajatdesikan at gmail.com
Sat Jun 1 12:06:26 CEST 2013

If the rest of your system is just water and ions, couple them separately
into another group and include it in your .mdp file.

On Sat, Jun 1, 2013 at 2:23 PM, neshat haq <neshathaq at gmail.com> wrote:

> Hello everyone
> I have a protein with covalently attached prosthetic group.
> Now while trying use thermostat I grouped the protein and prosthetic
> group though an index file as"Protein_pro"
> my Tc group is as"tc-grps        = Protein_pro Non-Protein"
> Now issuing the grompp for nvt step, following error is appearing
> Atom 1076 in multiple T-Coupling groups (1 and 2)
> This is very obvious that the prosthetic group will be in nonprotein index.
> The how to couple the prosthetic group and protein together with non
> protein.
> Or is it fine to couple a part of protein (prostheic group) with
> nonprotein.
> Any suggestion will be highly regarded.
> --
> Best regards
> Neshatul Haque
> PhD, Dpt of Biotechnology
> university of hyderabad
> --
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Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore

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