On 18/10/2011 5:40 AM, J. Nathan Scott wrote:
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?
Not currently, but it would not be hard to do.
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.
GROMACS is a normal C program, and can execute an external program.
Obviously this will still be inefficient if GROMACS was running in
parallel, since you have to have an I/O phase before and after the
external program and probably the other processors cannot do anything
useful. You would then have to re-distribute the charge vector over any
GROMACS parallel nodes.
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.
This would be slower still, but reliable and easy for proving the method.
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.
Ideally, GROMACS code would be linked with ZINDO and call the correct
function directly. This shouldn't be too bad since you merely need an
array of coordinates (and some other data which can be hard-coded
somehow) as input, and the charges out. You should probably get one or
other of the crude hacks working first, to judge how much value the
speed-up might have.
Mark
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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