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 topology).
So I wonder if this is just inevitable and we should live with it? Thanks, Yun On Wed, Nov 9, 2011 at 4:18 PM, Yun Shi <yunsh...@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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