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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========================================
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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