So I got it to work for my trimer by doing the following. <div><br class="webkit-block-placeholder"></div><div>1.) trjconv -f *.xtc -s *.tpr -pbc nojump -o out.xtc</div><div>2.) trjconv -f out.xtc -s *.tpr -pbc mol -center -boxcenter rect</div>
<div><br class="webkit-block-placeholder"></div><div>The first step unwraps the whole trajectory and the second step wraps it back up.</div><div><br class="webkit-block-placeholder"></div><div>Cheers,</div><div><br class="webkit-block-placeholder">
</div><div>Ilya</div><div><br class="webkit-block-placeholder"></div><div><br>-- <br>Ilya Chorny Ph.D.</div><br><div class="gmail_quote">On Tue, Apr 22, 2008 at 4:30 PM, Alan Dodd <<a href="mailto:anoddlad@yahoo.com">anoddlad@yahoo.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div style="font-family:times new roman, new york, times, serif;font-size:12pt">I've often found it necessary to do multiple trjconv steps to get the result I want. So in this case, I'd probably make sure my protein is genuinely centered in the box, then take that output .xtc and then make sure everything is whole and approximately in the box (-pbc whole).<div>
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<div style="font-size:12pt;font-family:times new roman, new york, times, serif">
<div style="font-size:12pt;font-family:times new roman, new york, times, serif">----- Original Message ----<br>From: Ilya Chorny <<a href="mailto:ichorny@gmail.com" target="_blank">ichorny@gmail.com</a>><br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Sent: Tuesday, April 22, 2008 11:52:23 PM<br>Subject: Re: [gmx-users] How to center my trimer in my simulation box.<br><br>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" rel="nofollow" target="_blank">ichorny@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="padding-left:1ex;margin:0pt 0pt 0pt 0.8ex;border-left:rgb(204,204,204) 1px solid">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>
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<div></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" rel="nofollow" target="_blank">X.Periole@rug.nl</a>> wrote:<br>
<blockquote class="gmail_quote" style="padding-left:1ex;margin:0pt 0pt 0pt 0.8ex;border-left:rgb(204,204,204) 1px solid">
<div>On Tue, 22 Apr 2008 14:14:19 -0700<br> "Ilya Chorny" <<a href="mailto:ichorny@gmail.com" rel="nofollow" target="_blank">ichorny@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="padding-left:1ex;border-left:rgb(204,204,204) 1px solid">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="padding-left:1ex;border-left:rgb(204,204,204) 1px solid">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" rel="nofollow" target="_blank">http://md.chem.rug.nl/~periole</a><br>
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