[gmx-users] problem with g_density

chris.neale at utoronto.ca chris.neale at utoronto.ca
Mon Oct 25 17:06:09 CEST 2010

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.


> 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.



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