[gmx-users] Groups in mdp file

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 1 05:12:15 CEST 2011

On 1/04/2011 2:06 PM, Sai Pooja wrote:
> On Thu, Mar 31, 2011 at 10:41 PM, Mark Abraham 
> <Mark.Abraham at anu.edu.au <mailto: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).

Describing the overall objective is usually a good idea. Sometimes one's 
candidate for a solution is not best and someone else knows it :-) Here, 
energy groups are the only reasonable solution.

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