[gmx-users] Re: sudden drop of minimal periodic distance

Yun Shi yunshi09 at gmail.com
Thu Nov 10 01:44:19 CET 2011

Sorry, I just found that even if I use a dodecahedron box with -d 1.2 nm,
the min periodic image dist still dropped abruptly to 0.172 or something
like this after around 35 ns or 30 ns (different trajectory with same

So I wonder if this is just inevitable and we should live with it?


On Wed, Nov 9, 2011 at 4:18 PM, Yun Shi <yunshi09 at gmail.com> wrote:

> Hello everyone,
> I am using g_mindist with -pi option to look at the minimal distance
> between periodic images of my protein-ligand system.
> It appears that after a certain amount of time (12 ns or 30 ns or ...),
> there would be a sudden drop of min distance from well above 2 nm to around
> 0.15 nm.
> I wonder if this is caused by the octahedral box I used in the MD
> simulation.
> But should I still be able to keep the part of trajectory before the
> sudden drop as valid so that I could do some analysis with my system?
> Thanks,
> Yun
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