Just to clarify.<div><br class="webkit-block-placeholder"></div><div>I would run</div><div><br class="webkit-block-placeholder"></div><div>trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro?</div><div><br class="webkit-block-placeholder">
</div><div>What would I run next?</div><div><br class="webkit-block-placeholder"></div><div>Thanks,</div><div><br class="webkit-block-placeholder"></div><div>Ilya</div><div><br><br><div class="gmail_quote">On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole <<a href="mailto:X.Periole@rug.nl">X.Periole@rug.nl</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="Ih2E3d">On Tue, 22 Apr 2008 14:14:19 -0700<br>
"Ilya Chorny" <<a href="mailto:ichorny@gmail.com" target="_blank">ichorny@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8x;border-left:1px #ccc solid;padding-left:1ex">
Hello,<br>
<br>
I am simulating a trimer in a membrane. In one of my simulation two of the<br>
monomers are on one side of the box and the other monomer is on the other<br>
side of the box. I tried using trjconv to center the whole thing in the<br>
center of my simulation cell but have failed miserably. I also searched<br>
around for about an hour and could not find anything.<br>
<br>
I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro.<br>
</blockquote></div>
first run<br>
trjconv -pbc nojump<div class="Ih2E3d"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8x;border-left:1px #ccc solid;padding-left:1ex">
Any advice?<br>
<br>
Thanks,<br>
<br>
Ilya<br>
<br>
-- <br>
Ilya Chorny Ph.D.<br>
</blockquote>
<br></div>
-----------------------------------------------------<br>
XAvier Periole - PhD<br>
<br>
NMR & Molecular Dynamics Group<br>
University of Groningen<br>
The Netherlands<br>
<a href="http://md.chem.rug.nl/~periole" target="_blank">http://md.chem.rug.nl/~periole</a><br>
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</blockquote></div><br><br clear="all"><br>-- <br>Ilya Chorny Ph.D.<br>
</div>