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