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?
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
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
