[gmx-users] sudden drop of minimal periodic distance

Yun Shi yunshi09 at gmail.com
Thu Nov 10 01:18:38 CET 2011

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

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?

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