[gmx-users] mdrun in gmx 4.5.1: how to reprogram periodic boundary conditions?
Mark.Abraham at anu.edu.au
Tue Nov 9 15:49:26 CET 2010
On 10/11/2010 1:32 AM, Adam Herbst wrote:
> 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 don't understand how that would work in concert with 3D PBC. It sounds
like you want water to "tunnel" across the membrane...
> 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,
PBC are only relevant where distances are being computed, so GROMACS
only cares during (off the top of my head) domain decomposition,
neighbourlist construction, bonded interactions, constraints, and maybe
load-balancing. Admittedly, that's half the code... There's no "one true
simulation cell" either, so there's no single place in the code that
"takes care of PBC".
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