Hello again, <br><br>I centered it and then did the calculation again for minimum image distance<br>but still it showed the same graph as without centering. I tried visualising it<br>using vmd but could not see any such clashes. since I am new to vmd<br>
I do not know whether it is possible to calculate such clashes if at all <br>in vmd? I am using dodecahedron box. can it be visualised as it is in vmd?<br><br>Thank you<br>With regards<br>Kavya<br><br><div class="gmail_quote">
On Wed, Sep 21, 2011 at 5:12 PM, Kavyashree M <span dir="ltr"><<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Thanks.<div><div></div><div class="h5"><br><br><div class="gmail_quote">On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div></div><div><br>
<br>
Kavyashree M wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear users,<br>
<br>
I was trying to simulate a protein dimer covalently bond with<br>
a disulphide bond (230+230 aa long). I used usual protocol<br>
as used for simulation of a monomeric protein, using gromacs-<br>
4.5.3, dodecahedron box, tip4p water model and protein to<br>
box distance of 1 (-d in editconf). In the middle of the simulation<br>
when i checked for minimum image violation there was huge<br>
clashes. I am extremely sorry I have been asking regarding this<br>
many times but in this it is a dimer and I am not sure what mistake<br>
I have done because this happened while simulating another dimer<br>
also though not sever. Hence I seek some guidance from this<br>
community regarding the problem. I attach the graph herewith.<br>
Kindly help. Let me know if I need to give any other information.<br>
<br>
</blockquote>
<br></div></div>
Please see my post from yesterday for a more detailed reply to this exact same type of question. I am beginning to suspect there's a problem with g_mindist, but I have no solid evidence for that claim, just a hunch. It looks like your protein crosses a periodic boundary and that messes up the calculation. Please center the protein in the box with trjconv -center and re-analyze to see if there are any differences.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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