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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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