Darrell Koskinen wrote:
Hi Mark,
No, I am not trying to build a random number generator and hope that I
am not moving in this direction : )
My definition of adsorption energy would be the difference in energy
when two species are at an infinite distance and the energy when these
species are at an equilibrium distance from each other.
OK, but I think you need to measure a free energy change, using (for
example) a PMF generated by the pulling code in GROMACS.
I think the way in which I can measure this energy difference would be
to subtract the LJ (LR) energy between an ammonia molecule and the
graphene sheet (where the distance between the molecule and the graphene
sheet is large) from the LJ (SR) energy between an adsorbed ammonia
molecule and the graphene sheet.
That assumes an unrealistic independence of the forcefield
contributions. Why would energy not partition over bonded and Coulombic
interactions also?
Also, the distinction between LR and SR is merely to do with your
twin-range cut-off choices (read manual!). The adsorption process is a
transition from no interaction (i.e. outside the LR cutoff) to physical
contact. The total LJ interaction energy (if that means anything!) will
be partitioned between LR and SR according to distance from the surface.
I am not aware that OPLS-AA was parameterized to produce such values,
but would appreciate your comments.
I know nothing about OPLS-AA, but would guess that it wasn't
parameterized for graphite, gaseous ammonia or to reproduce adsorption
energies. I think you'd have to demonstrate (through simulation or
literature reference) suitable behaviour of graphite and gaseous ammonia
on their own before trying to simulate them together. If there's some
kind of experimental observable about the behaviour of adsorbed ammonia
on graphite that you could reproduce, that would be a useful indicator
that the force field is doing OK. Absent that, you might just have that
random number generator :-)
Mark
Message: 2
Date: Thu, 12 Nov 2009 10:42:24 +1100
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4afb4be0.1020...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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" <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: <4aee4387.40...@vt.edu>
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" <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: <4aee27f0.50...@vt.edu>
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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