[gmx-users] Groups in mdp file

Sai Pooja saipooja at gmail.com
Fri Apr 1 05:06:28 CEST 2011

On Thu, Mar 31, 2011 at 10:41 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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.

Well the idea is to modify the hamiltonian for only a subset of atoms and
apply hamiltonian replica exchange. I was hoping defining energy group could
be a good way to apply this(obv it would requires other changes too).

> Mark
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