[gmx-users] Adsorption energy of a single molecule

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 2 01:29:36 CET 2009

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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