[gmx-users] Adsorption energy of a single molecule

Justin A. Lemkul jalemkul at vt.edu
Sun Nov 1 13:17:24 CET 2009

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.


> Thanks.
> Darrell
>> Date: Thu, 29 Oct 2009 14:06:27 -0400
>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>> Subject: Re: [gmx-users] Adsorption energy of a single molecule
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <4AE9D9A3.9080004 at vt.edu>
>> Content-Type: text/plain; charset=UTF-8; format=flowed
>> darrellk at ece.ubc.ca 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


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