[gmx-users] Groups in mdp file
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:
> 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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