The problem is considerably worse than that. g_density is incorrect
for every bin in the NPT ensemble. First, you have fluctuations in the
z dimension. Second, g_density determines the bin as: slice = (int)(z
/ (*slWidth)); in calc_density() after wrapping coordinates around
periodic z in all gromacs versions that I have seen, including v4.0.7
and v4.5.1. Thus, even the values near the bilayer center that appear
to be ok are actually incorrect due to the addition of
periodic-fluctuation-based noise. I've mentioned this on-list
previously. Given this problem, the error introduced to g_hbond in the
gmx4.5 series, and the lack of a proper test suite, I suggest always
writing your own code that can test at least two frames of the output
of any analysis program (even if your code only takes input as pdbs
and runs slowly) so that you can develop some confidence in the output
of the gromacs analysis tool.
Chris.
You're not
seeing complete mixing of your two species, but there is some diffusion
between the phases, otherwise both of your particles should drop to exactly
zero density on either side of the box middle, wouldn't they?
No, not if there are undulations of the interface.
Cheers,
Tsjerk
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