Dear Sir,<br><br> Thanks for your patient reply Sir.<br><br>With Regards<br>M. Kavyashree<br><br><div class="gmail_quote">On Sat, Jun 11, 2011 at 9:57 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi Kavya,<br>
<div class="im"><br>
>> It is absolutely necessary that the molecules be whole, and in the<br>
>> case of multimers, correctly assembled.<br>
><br>
> But if there is only one polymer (protein) with water in the system<br>
> then also is it necessary to use nojump or mol in trjconv?because<br>
> in one of the mails -<br>
><br>
> <a href="http://lists.gromacs.org/pipermail/gmx-users/2010-October/055320.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2010-October/055320.html</a><br>
><br>
> there was a discussion regarding this topic. So I wanted to<br>
> ensure regarding that aspect. Molecule after simulation<br>
> crosses the box boundary in the simulation I have done, So<br>
> if I processed analyzing with the native .xtc file there will be<br>
> a problem? But in this case its a single intact protein molecule<br>
> in water.<br>
<br>
</div>That post concerns -pbc nojump. My reply to you was about having<br>
molecules in one piece. They're different things. Gromacs nowadays<br>
doesn't care about molecules being whole in the trajectory file, and<br>
happily writes them in pieces. So you can't be confident you can use<br>
the trajectory as is.<br>
<div><div></div><div class="h5"><br>
Cheers,<br>
<br>
Tsjerk<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>
--<br>
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