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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