Darrell Koskinen wrote:
Hi Justin,
In my simulation, I have just over 100 ammonia molecules and, of these
molecules, 10 to 20 adsorb onto the graphene sheet. I initially thought
that I would need to tag each one of the ammonia molecules, since I
would not know, in advance of running the simulation, which of these
molecules would adsorb.
Are you suggesting that, after the initial simulation run, which uses an
index file "index.ndx" and is comprised of three components {System,
Grph, NH3}, I run make_ndx again to assign each adsorbed molecule to its
own index, execute "mdrun -rerun mdtraj.trr -s mdtopol.tpr", where
mdtraj.trr and mdtopol.tpr are the output of the initial simulation, and
then use g_energy to analyze the energies between the groups?
I don't know what Justin suggested, but a re-run with each ammonia in
its own energy group ought to allow you to observe absorption events
from the individual energy profiles over time.
Mark
Date: Sun, 01 Nov 2009 07:17:24 -0500
From: "Justin A. Lemkul" <jalem...@vt.edu>
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4aed7c54.2080...@vt.edu>
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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" <jalem...@vt.edu>
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4ae9d9a3.9080...@vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed
darre...@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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