[gmx-users] Adsorption energy of a single molecule

Darrell Koskinen darrellk at ece.ubc.ca
Mon Nov 2 03:24:42 CET 2009

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?

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?




Date: Sun, 01 Nov 2009 19:29:36 -0500
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: <4AEE27F0.50301 at 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 


-- ======================================== 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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