[gmx-users] Membrane protein tutorial

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 9 07:24:47 CEST 2009

Pawan Kumar wrote:
> Hello sir,
> Thanks for your reply.
> I have used this .mdp file. Is there anything wrong in the mdp file 
> which I am using ?

No, but the manner in which you are using groups in that .mdp file isn't 
consistent with the way you've defined them in your index file - like I 
said last time:

>     You can't have the same atom in multiple groups used for the same
>     purpose within mdrun (e.g. T-coupling or energy). I guess you've
>     constructed your index file in a manner that is inconsistent with
>     your use of it.

The GROMACS error message could certainly be more helpful here - naming 
the groups and what you're using them for, but in your case this is not 
impeding your troubleshooting.


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