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

[Tsjerk Wassenaar]

Hi Yun,

Well, within 2 nm periodic images can influence each other through ordering
of water. But how much that will affect your results and how relevant it is
for the properties you're after is hard to tell. I think most people will
just continue with analysis, saying that there have been no direct
interactions.

Cheers,

Tsjerk

On Nov 10, 2011 6:42 PM, "Yun Shi" <yunshi09 at gmail.com> wrote:

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_mindis...
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