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<br><br><br><div class="gmail_quote">On Wed, Nov 9, 2011 at 4:18 PM, Yun Shi <span dir="ltr"><<a href="mailto:yunshi09@gmail.com">yunshi09@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hello everyone,<br><br>I am using g_mindist with -pi option to look at the minimal distance between periodic images of my protein-ligand system.<br>
<br>It appears that after a certain amount of time (12 ns or 30 ns or ...), there would be a sudden drop of min distance from well above 2 nm to around 0.15 nm.<br>
<br>I wonder if this is caused by the octahedral box I used in the MD simulation. <br><br>But should I still be able to keep the part of trajectory before the sudden drop as valid so that I could do some analysis with my system?<br>
<br>Thanks,<br><font color="#888888">Yun<br>
</font></blockquote></div><br>