Dear Mark<br><br>That is my thought too.To test this possibility, I created a mdp file without PBC and use trjconv -pbc nojump to make whole protein. >From visualization in UCSF Chimera, the trajectory looks fine. But I still have some snapshot that have very high vdw energy.<br>
<br>best<br><br>dawei<br><br><div class="gmail_quote">On Wed, Aug 10, 2011 at 11:12 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im">On 11/08/2011 12:29 AM, Da-Wei Li wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Gromacs users:<br>
<br>
I recently tried some MM/PBSA stuff using the rerun function of mdrun and GBSA model. All water molecules are stripped off the trajectory file.<br>
<br>
However, when I examine the different energy term, it is disturbing that short range vdw energy of some snapshot are very high (> 1000 kj/mol) while others snapshots typically have a value around -2000 kj/mol.<br>
</blockquote>
<br></div>
Something is badly wrong - perhaps your treatment of periodicity in the rerun - but we don't have anywhere near enough information to know.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
It is more disturbing that if I do a fitting or pbc nojump on the trajectory first, I will get very different short range vdw for some of the snapshots. All other energy terms are un-affected.<br>
<br>
I believe fitting or no-jump processing shall not change the energy at all.<br>
<br>
Any one has idea about this?<br>
</blockquote>
<br></div>
As above.<br>
<br>
Mark<br><font color="#888888">
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