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<a class="moz-txt-link-abbreviated"
href="mailto:paloureiro@biof.ufrj.br">paloureiro@biof.ufrj.br</a>
wrote:
<blockquote cite="mid1132588118.4381ec56d402c@webmail.biof.ufrj.br"
type="cite">
<pre wrap="">Hi!
I have a system of "n" molecules in the liquid state. I picked one type of atom
and used it as an input group (with "n" atoms) in ED analysis.
1) How do I extract the mean-square displacement along a certain eigenvector?
2) How do I get rid of jumps across the box? I have played with trjconv -pbc
(whole/nojump/inbox) with no success...
</pre>
</blockquote>
Use -center tric together with -pbc inbox. Center the protein or one
chain of nucleic acid will let you get a complete "amber".<br>
<blockquote cite="mid1132588118.4381ec56d402c@webmail.biof.ufrj.br"
type="cite">
<pre wrap="">
Regards.
Pedro.
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</pre>
</blockquote>
<br>
<div class="moz-signature">-- <br>
<i>Regards,</i><br>
Yang Ye<br>
<small><i>Computational Biology Lab<br>
School of Biological Sciences<br>
Nanyang Technological University<br>
Singapore<br>
Tel: 6316-2884<br>
</i></small>
</div>
<br>
<div class="moz-signature">-- <br>
<i>Regards,</i><br>
Yang Ye<br>
<small><i>Computational Biology Lab<br>
School of Biological Sciences<br>
Nanyang Technological University<br>
Singapore<br>
Tel: 6316-2884<br>
</i></small>
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