<p>Hi Yun,</p>
<p>Make sure to remove jumps from the trajectory (trjconv -pbc nojump) before using g_mindist.<br>
Also visually check a frame that is reported to have closed contacts.</p>
<p>Hope it helps,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Nov 10, 2011 1:45 AM, "Yun Shi" <<a href="mailto:yunshi09@gmail.com">yunshi09@gmail.com</a>> wrote:<br><br>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).<br>
<br>So I wonder if this is just inevitable and we should live with it?<br><br>Thanks,<br>Yun<p><font color="#500050">
On Wed, Nov 9, 2011 at 4:18 PM, Yun Shi <<a href="mailto:yunshi09@gmail.com">yunshi09@gmail.com</a>> wrote:
>
> Hello everyone,
>
> I am ...</font></p><br>--<br>
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