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On 26/09/2011 10:02 PM, Kavyashree M wrote:
<blockquote
cite="mid:CAPLGqjpLtAH=bKvUhVw04veBvEO1FFTNhPm9sDRX9GzsvsBfHw@mail.gmail.com"
type="cite">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. </blockquote>
<br>
Have you followed the kind of workflow suggested here? <a
href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a><br>
<br>
<blockquote
cite="mid:CAPLGqjpLtAH=bKvUhVw04veBvEO1FFTNhPm9sDRX9GzsvsBfHw@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
Yes, one can be visualized, but some preparation with trjconv -ur
compact (as hinted at in trjconv -h) is a good idea.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAPLGqjpLtAH=bKvUhVw04veBvEO1FFTNhPm9sDRX9GzsvsBfHw@mail.gmail.com"
type="cite"><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
moz-do-not-send="true" 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 class="h5"><br>
<br>
<div class="gmail_quote">On Wed, Sep 21, 2011 at 5:07 PM,
Justin A. Lemkul <span dir="ltr"><<a
moz-do-not-send="true" 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><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>
========================================<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 moz-do-not-send="true"
href="http://vt.edu" target="_blank">vt.edu</a> |
(540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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