Hi Tsjerk,<br><br>Thanks for the advice. <br><br>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.<br>
<br>This is not "ideal", but I wonder if it's still OK to use this trajectory?<br><br>Thanks,<br>Yun<br><br><br>Message-ID:<br>
<<a href="mailto:CABzE1Sg24mU7zSH7aSvMfAiNrjsMvGKOmG3uy-iXfTOKWVr9_A@mail.gmail.com">CABzE1Sg24mU7zSH7aSvMfAiNrjsMvGKOmG3uy-iXfTOKWVr9_A@mail.gmail.com</a>><br>
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<br>
Hi Yun,<br>
<br>
Make sure to remove jumps from the trajectory (trjconv -pbc nojump) before<br>
using g_mindist.<br>
Also visually check a frame that is reported to have closed contacts.<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<br>
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,<br>
the min periodic image dist still dropped abruptly to 0.172 or something<br>
like this after around 35 ns or 30 ns (different trajectory with same<br>
topology).<br>
<br>
So I wonder if this is just inevitable and we should live with it?<br>
<br>
Thanks,<br>
Yun<br>
<br>
On Wed, Nov 9, 2011 at 4:18 PM, Yun Shi <<a href="mailto:yunshi09@gmail.com">yunshi09@gmail.com</a>> wrote: > ><br>
Hello everyone, > > I am ...<br>
<br>
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