Erik and Mark: Thanks for your help, I will begin diving into the code
today.
Mark, if everything went ideally (which things don't always), I would
use the force tables to compute the total SR electrostatic force on
each atom in a specific group (around 2 to 7 atoms). The same goal can
be accomplished by running a trajectory and then rerunning it to
calculate the electrostatic forces exclusively. This is what we have
done before, but saving the necessary trajectory file for our current
system has gotten too costly. Instead, I am hoping to collect the
forces and save those exclusively at each timestep (along with
positions at larger intervals). So far it has seemed that Gromacs
creates a separate coulombic and LJ table, but uses a combined table to
actually compute the forces. So it should be capable of computing the
simple ES force on the fly and saving them. Any suggestions on a better
tactic?
Justin
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