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leila karami skrev 2010-08-31 14.48:
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<p class="MsoNormal">Dear gromacs users</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I did simulation of protein-dna complex in a
box with size
7,7,7. There are 5000 water molecule in this box. After full md
simulation, I
need a pdb or gro file containing only water molecules being
exactly environment
of pr-dna complex and not water molecules being in edges or rest
of box.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Is there any way to do that?</p>
</blockquote>
Use trjorder which orders your water molecules according to their
distance to the solute. Then remove tha last few thousand waters in
a text editor.<br>
<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
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