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

[Yun Shi]

Hi Tsjerk,

Thanks for the advice.

After I did the nojump conversion of trajectories, there were still quite a
few frames with min. dist. under 2.0 nm, but all of them were above 1.4 nm,
which I set for rvdw.

This is not "ideal", but I wonder if it's still OK to use this trajectory?

Thanks,
Yun


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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,

Tsjerk

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
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 <yunshi09 at gmail.com> wrote: > >
Hello everyone, > > I am ...

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