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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