[gmx-users] mdrun in gmx 4.5.1: how to reprogram periodic boundary conditions?

Adam Herbst adh38 at cornell.edu
Tue Nov 9 15:32:27 CET 2010

I'd like to modify how the periodic boundary conditions are implemented when
simulating a box with mdrun (the md integrator).  Specifically, with two
lipid bilayer membranes in the box, I'd like to make it possible for water
molecules to move from the space between the membranes to the space outside
them.  I know that the function stack looks something like: main() [mdrun.c]
-> mdrunner() [runner.c] -> do_md() [md.c].  Also, it says in the
programmer's guide (
that do_force() [sim_util.c] or dd_partition_system() [domdec.c] take care
of periodic boundary conditions, depending on whether MPI/domain
decomposition are enabled.  I verified with printf statements that the
do_force() function is being executed in every step of my simulation.  And
in the code for these functions I see things that look relevant, but I can't
seem to find exactly where it says that, e.g., an atom going out one side of
the box should come back in the other side.  Is anyone familiar with this?
 Thanks a lot,

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