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On 11/08/2011 1:45 AM, Da-Wei Li wrote:
<blockquote
cite="mid:CAFs1QTd_QyWzupFrk9wGgWkKYUykK5D2C0vF9VKiFBq8BWpYAw@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
Not unless you can show me a shell script and .mdp file that can
take your original trajectory, do my suggested procedure and produce
your observed output. Otherwise, the chance of user error is a
thousand times more likely than a GROMACS problem.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAFs1QTd_QyWzupFrk9wGgWkKYUykK5D2C0vF9VKiFBq8BWpYAw@mail.gmail.com"
type="cite"><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 moz-do-not-send="true"
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
moz-do-not-send="true"
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>
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