Dear Mark<br><br>Could you please help me out? I can send you the trajectory (1000 snapshot in pdb format), mdp, topol file. I use Gromacs-4.5.3.<br><br>I checked the pdb file in UCSF Chimera and didn't find any crash. I have about 10 snapshot that has high vdw energy.<br>
<br>best,<br><br>dawei<br><br><br><br><div class="gmail_quote">On Wed, Aug 10, 2011 at 11:32 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 bgcolor="#FFFFFF" text="#000000"><div class="im">
On 11/08/2011 1:18 AM, Da-Wei Li wrote:
<blockquote type="cite">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>
</blockquote>
<br></div>
If all you've done is strip water, make molecules whole with trjconv
-nojump from a reference configuration that had whole molecules, and
use pbc = no in the .mdp file, then that sounds impossible.<br><font color="#888888">
<br>
Mark</font><div class="im"><br>
<br>
<blockquote type="cite">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" target="_blank">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>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><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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