[gmx-users] Re: Determining energies between a solute and solvent

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 23 21:59:33 CET 2012

Fabian Casteblanco wrote:
> Thanks.  This helps.   One more question, is it possible to further
> break down the energy interactions between a piece of a protein and
> another piece of the solvent?   For example, if I wanted the Cou and
> vdw interactions specifically for an  -OH group on a solvent and some
> chain on the solute.  I know how to do this using make_ndx for g(r)
> plots but I don't see how you can apply it to energygrps on the *.mdp
> file.

It is possible, just a little more complicated.  The use of energygrps requires 
that the groups be non-overlapping, so if you have some fragments you want to 
consider, you have to create complementary groups for all the rest, i.e.:

enerygrps = fragment Protein_not_fragment sol_fragment SOL_not_sol_fragment



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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