[gmx-users] Updating charges on-the-fly

J. Nathan Scott scottjn at chemistry.montana.edu
Mon Oct 17 20:40:48 CEST 2011

Hello fellow GMX users,

I've been digging in the archives and haven't yet found a good response to
this question, so I thought I'd ask again, since I see from a post just last
month others are still interested in this subject as well. Is it possible in
Gromacs to periodically update/change the charges on a given molecule or
residue during the course of a simulation?

What I am envisioning is having a production simulation running, and then
every "x" amount of time, the current checkpoint file gets read and
processed by an external routine that calculates charges on the residue or
molecule of interest, which are then fed back into Gromacs to continue the
run. Is it possible to execute an external program from within a Gromacs
simulation? I know this functionality must be in there somewhere, since
Gromacs can communicate with external QM software, but I'm not sure if a
charge modification scheme could make use of the same built-in I/O methods.

Is such a scheme possible? I realize an alternative method would be to stop
the run, do some calculation to recalculate the charges, and then perhaps
use some simple code to modify the .top file directly, and finally grompp
out a new tpr file and continue the run. Lather, rinse, repeat. I'm guessing
this could be rather slow because of needing to call grompp over and over
and the need to continually restart the simulation.

For what it's worth, my interest lies mainly in excited state chromophores
and I'd be using modified ZINDO code to calculate charges every x number of
steps. This calculation is *very* fast, even for large chromophores,
therefore my focus on other performance bottlenecks.

I would be extremely grateful for any feedback on this subject, particularly
from anyone who has done a similar thing successfully and cares to share any
tips or code.

J. Nathan Scott, Ph.D.
Postdoctoral Fellow
Department of Chemistry and Biochemistry
Montana State University
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