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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Nov 10 06:49:30 CET 2011

Hi Yun,

Make sure to remove jumps from the trajectory (trjconv -pbc nojump) before
using g_mindist.
Also visually check a frame that is reported to have closed contacts.

Hope it helps,


On Nov 10, 2011 1:45 AM, "Yun Shi" <yunshi09 at gmail.com> wrote:

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 ...

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