On 10/11/2010 1:32 AM, Adam Herbst wrote:
Hi,
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
(http://www.gromacs.org/Developer_Zone/Programming_Guide/Programmer's_Guide#home
<http://www.gromacs.org/Developer_Zone/Programming_Guide/Programmer%27s_Guide#home>)
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".
Mark
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