<html><body><div style="color:#000; background-color:#fff; font-family:verdana, helvetica, sans-serif;font-size:12pt"><div><span>Thank you very much.</span></div><div><br><span></span></div><div><span class="tab">Best Regards</span></div><div><span class="tab">Sara<br></span></div><div><br></div> <div style="font-family: verdana, helvetica, sans-serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Saturday, December 24, 2011 1:48 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] micelle clustering<br> </font> <br>
<div id="yiv1380223337">
<div>
On 12/24/2011 8:01 PM, mohammad agha wrote:
<blockquote type="cite">
<div style="color:#000;background-color:#fff;font-family:verdana, helvetica, sans-serif;font-size:12pt;">
<div>Dear GROMACS users</div>
<div><br>
</div>
<div>I want to analysis of 2 micelles that are created in one
simulation, when I view output of trajectory by vmd or ngmx:</div>
<div>ngmx -f md.trr -s md.tpr</div>
<div>has been created 2 micelles, then I try to micelle
clustering by: <br>
</div>
<ol>
<li><code>trjconv -f md.xtc -o a_cluster.gro -e 0.001 -pbc
cluster</code></li>
<li><code>grompp -f md.mdp -c a_cluster.gro -o a_cluster.tpr</code></li>
<li><code>trjconv -f md.xtc -o a_cluster.xtc -s a_cluster.tpr
-pbc nojump</code></li>
</ol>
<div><span></span></div>
<div>but when I view cluster.xtc, just has been created one
micelles and remainder of monomers have been collected in
different places in 3 or 4 groups!!!</div>
<div><br>
</div>
<div>May I know why do this occur? and where is my mistake? and
what should I do, please?</div>
</div>
</blockquote>
<br>
Hard to say, because we don't know what your objective is. You need
to be very clear in your own mind what you want to see if the
underlying behaviour is that the two micelles move away from each
other in one cell and meet each other across another boundary, and
design a workflow accordingly.<br>
<br>
I suggest you read trjconv -h carefully and consider the workflow
advice here http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions<br>
<br>
Mark<br>
<br>--
<br>This message has been scanned for viruses and
<br>dangerous content by
<a rel="nofollow" target="_blank" href="http://www.mailscanner.info/"><b>MailScanner</b></a>, and is
<br>believed to be clean.
</div>
</div><br>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br> </div> </div> </div></body></html>