Hi,<div>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 (<a href="http://www.gromacs.org/Developer_Zone/Programming_Guide/Programmer's_Guide#home">http://www.gromacs.org/Developer_Zone/Programming_Guide/Programmer's_Guide#home</a>) 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,</div>
<div><br></div><div>Adam</div>