Darrell Koskinen wrote:
Hi Justin,
So when I create the index file with the molecule and the graphene sheet
and run g_energy, is the adsorption energy between the adsorbed molecule
and the graphene sheet the LJ (SR) energy? And will this energy be just
the interaction energy between the adsorbed molecule and the graphene
sheet (i.e. does the creation of the new index file and executing -rerun
cause g_energy to exclude the energies between the other molecules and
the graphene sheet)?
Unless you have set some special energygrp_excl in the .mdp file, then nothing
should be excluded; the use of energygrps simply decomposes the energy terms
into the species of interest.
As for what the adsorption energy is, it may well be LJ(SR), provided there are
no Coulombic terms to worry about, but I don't know anything about your
parameters, so I can't say definitively.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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