[gmx-users] Groups in mdp file

[Mark Abraham]

On 1/04/2011 1:30 PM, Sai Pooja wrote:
> Hi,
> This is regarding the energygroups that one can use in the mdp file 
> for tracking energy. Are these the groups defined in the index file?

Yes, the groups are defined there (or created by default if an index 
file is not supplied) and specified as energy groups in the .mdp file.

> I want to know if I can define a subset of atoms in the index file and 
> track its energy.

Yes. Whether it means anything is another matter.

Mark