So I got it to center my protein (using -pbc nojump) and keep the trimer and the membrane in tact but it completely destroyed my water. I was hoping I could get the whole simulation box back with the protein in the center. Is that possible?<br>
<br>Thanks,<br><br>Ilya<br><br><br><div class="gmail_quote">On Tue, Apr 22, 2008 at 3:25 PM, Ilya Chorny <<a href="mailto:ichorny@gmail.com">ichorny@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Just to clarify.<div><br></div><div>I would run</div><div><br></div><div>trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro?</div><div><br>
</div><div>What would I run next?</div><div><br></div><div>Thanks,</div><div><br></div><div>Ilya</div><div><div><div></div><div class="Wj3C7c"><br><br><div class="gmail_quote">On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole <<a href="mailto:X.Periole@rug.nl" target="_blank">X.Periole@rug.nl</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>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="border-left: 1px solid rgb(204, 204, 204); 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><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); 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/%7Eperiole" target="_blank">http://md.chem.rug.nl/~periole</a><br>
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</blockquote></div><br><br clear="all"><br></div></div>-- <br>Ilya Chorny Ph.D.<br>
</div>
</blockquote></div><br><br clear="all"><br>-- <br>Ilya Chorny Ph.D.<br>