Darrell Koskinen wrote:
Hi Justin,
Thanks for the suggestion. I looked through the GROMACS manual and the
only method I can see of obtaining the adsorption energy between an
adsorbed ammonia molecule and the graphene sheet would be to create an
index file that assigns a separate index for each ammonia molecule, run
the simulation, and then run "gmxdump -e mdener.edr" to view the energy
between the adsorbed ammonia molecule and the graphene sheet. Is this
the method you are suggesting or is there a different method of
obtaining this information?
From your original message, I got the impression that only a few of your
ammonia molecules were adsorbed. In this case, a better approach might be to
identify the molecules that adsorbed in your original simulation, create groups
for those individually, the graphene sheet, and then the rest of your ammonia.
Then use mdrun -rerun with your new .tpr file, and g_energy (not gmxdump) to
analyze the energies between the various groups.
-Justin
Thanks.
Darrell
Date: Thu, 29 Oct 2009 14:06:27 -0400
From: "Justin A. Lemkul" <[email protected]>
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=UTF-8; format=flowed
[email protected] wrote:
Dear GROMACS Gurus,
Is it possible to determine the adsorption energy of a single
molecule in
a simulation? My simulation has a large number of gas phase molecules
distributed throughout a box with some molecules adsorbed on a graphene
sheet. I would like to compare the adsorption energy of a single
molecule to that reported in research papers.
You should be able to study interactions between individual molecules
by using energygrps and an appropriate index file.
-Justin
Thanks.
Darrell
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--
========================================
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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