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?
Not necessarily, unless the force field was parameterized to produce
such values. First, seek to define what you mean by adsorption (free)
energy, then consider how a simulation might measure that. Then,
consider whether any force fields exist that might achieve that. Then,
test it on a case where you have experimental data.
Other procedures run a much higher risk of producing an expensive random
number generator :-)
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)?
Creating an energy group causes mdrun -rerun to report the fraction of
the total nonbonded energies that are due to intra- and inter-group
interactions. See manual section 3.3
Mark
Date: Sun, 01 Nov 2009 21:27:19 -0500
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=ISO-8859-1; format=flowed
Darrell Koskinen wrote:
Hi Justin,
Since I cannot use the original .tpr file, then do I need to run
grompp with the new index file to create a "new" .tpr file,
"mdtopolnew.tpr"? I assume I then need to modify the energygrps line
within the .mdp file to include these new energy groups and then
execute "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr". Is this correct?
Yes, that is the point of the -rerun function.
Does executing "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr" cause a
molecular dynamics simulation to run once again? If so, then will the
exact same molecules that adsorbed on the first MD run be the same
ones that adsorb on the second MD run?
The original coordinates are used to re-calculate the energies. No
new simulation is performed.
-Justin
Thanks.
Darrell
***********************************************************************
***********************************************************************
Date: Sun, 01 Nov 2009 19:29:36 -0500
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=ISO-8859-1; format=flowed
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?
Almost. You can't use the original .tpr file if you are trying to
establish new energy monitoring groups. Hence the point of making a
new .mdp file. So, re-run the old trajectory with the new .tpr file
to take advantage of the new groups.
-Justin
-- ======================================== 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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