[gmx-users] Adsorption energy of a single molecule

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 12 00:26:49 CET 2009

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 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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