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On 05/30/2011 03:36 PM, Kavyashree M wrote:
<blockquote
cite="mid:BANLkTin=ewdT=_oMox9JzXAWhNZs7J=6GQ@mail.gmail.com"
type="cite">Hello Sir, <br>
<br>
I saw the 21824th frame, it dint look unusually stretched when<br>
I superposed against the initial pdb file. there atoms were
hydrogen <br>
atoms of two lysine residues.. And in the entire strttch of 100ns
simulation <br>
this is the only periodic image interaction observed, Is it
possible to correct <br>
it now. or should I have to redo the simulation again??<br>
</blockquote>
<br>
We can't tell from the above description. Only you have the
information about whether they really made such contact, and whether
that's a serious problem. Make sure your observations above are not
artefacts of periodicity.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTin=ewdT=_oMox9JzXAWhNZs7J=6GQ@mail.gmail.com"
type="cite">Kindly reply..<br>
<br>
Thank you<br>
With regards<br>
M. Kavyashree<br>
<br>
<div class="gmail_quote">
On Sun, May 29, 2011 at 5:40 PM, Tsjerk Wassenaar <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</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;">
Hi Kavya,<br>
<div class="im"><br>
> "shortest periodic distance is 1.39714 (nm) at time
21824 (ps),<br>
> between atoms 2062 and 3688"<br>
> where 2062 is a protein atom and 21824 is a water
molecule.<br>
<br>
</div>
21824 is the time in ps at which the two atoms indicated, 2062
and<br>
3688, are at the short distance given. You can dump the frame
with<br>
trjconv and have a look. Probably your molecule stretched, or
you<br>
solvated in a rectangular box and the protein rotated. In the
first<br>
case, set a larger distance, in the second, use a rhombic<br>
dodecahedron.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and
Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
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