[gmx-users] Adsorption energy of a single molecule

[Justin A. Lemkul]

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

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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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