Hi Sulatha,<br><br>Did you install gromacs yourself or are you using a system wide installation?<br><br>A. I installed myself<br><br>In that case you go into the directory where you have put the gromacs source code and put the modified version of gmx_trjconv.c in the subdirectory src/tools. Then you go into that directory and type 'make trjconv' <br>
<br>B. I just used what was available already<br><br>If you're good friends with the system administrator you can ask him/her to compile the modified trjconv, as under A.<br>Otherwise, you'd better install gromacs yourself as explained on the gromacs site and then go to A.<br>
<br>Hope it helps,<br><br>Tsjerk<br><br><div class="gmail_quote">On Thu, Jun 30, 2011 at 10:10 AM, gregory megariotis <span dir="ltr"><<a href="mailto:gmegariotis@yahoo.gr">gmegariotis@yahoo.gr</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font: inherit;" valign="top">
Dear Sulatha, <br><br>You can try the command <span></span><span style="font-style: italic;">trjconv -f a.xtc -o
b.gro -pbc cluster -e 0.002</span> with GROMACS 4.5.4. <br><br>Best regrds <br><br>Grigoris<br><br>--- Στις <b>Πέμ., 30/06/11, ο/η sulatha M. S <i><<a href="mailto:mssulatha@gmail.com" target="_blank">mssulatha@gmail.com</a>></i></b> έγραψε:<br>
<blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>Από: sulatha M. S <<a href="mailto:mssulatha@gmail.com" target="_blank">mssulatha@gmail.com</a>><br>Θέμα: [gmx-users] micelle clustering<br>
Προς: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>Ημερομηνία: Πέμπτη, 30 Ιούνιος 2011, 9:18<div><div></div><div class="h5"><br>
<br><div>
<p>Hi all,<br></p><p>I have simulated a system of randomly dispersed surfactants in
water using gromacs (4.0.7) for about 100 ns MD. Micelles are formed after
around 40 ns. <span> </span>I am using a time step of
0.002 fs with xtc files written every 500 steps. For analyzing the micellar
properties, I tried the commands given in </p>
<pre><a rel="nofollow" href="http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering" target="_blank">http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering</a></pre>
<p>and also looked at the various posts given on this topic, (specifically
Chris Neale’s and Tsjerk’s mails).</p>
<p>As posted by Chris Neale, I tried using the commands,</p>
<pre>1. trjconv -f a.xtc -o b.gro -pbc cluster -e 0.001 (make sure to just<span> </span></pre><pre>get one frame)</pre><pre>2. grompp -f a.mdp -c b.gro -p a.top -o b.tpr</pre><pre>3. trjconv -f a.xtc -o b.xtc -s b.tpr -pbc nojump</pre>
<p> </p>
<p>Also mentioned in Tsjerk’ post that</p>
<pre>“When doing so, be sure to use a frame which is close enough to the</pre><pre>starting frame in terms of the coordinates. -pbc nojump works based on</pre><pre>the coordinates and if you use a reference which doesn't match the</pre>
<pre>starting frame close enough everything can get really messed up”.</pre><pre> </pre><pre> </pre>
<p>I tried the command 1 with </p>
<p><span> </span>trjconv -f a.xtc -o
b.gro -pbc cluster -e 0.002 </p>
<p>and also</p>
<p><span> </span>trjconv -f a.xtc -o
b.gro -pbc cluster –dump X (where x=2, 4, 6, 8 etc..)</p>
<p>The program gets into a never ending loop. </p>
<p>I also tried the command 1 on a later part of the trajectory
(after 40 ns), there also the program enters in a indefinite loop.</p>
<p>I will greatly appreciate any help on how to go about doing
this specifically which frame (for dump or –e argument) .<span> </span>Please guide me on this.</p>
<p>I also downloaded the modified trjconv.c<span> </span>by Tsjerk (in one of his posts on micelle
clustering), but do not know where to incorporate this. I need some help on how
to use this modified trjconv code.</p><p><br></p><p>Thanks for any help or clue,<br></p><p>Sulatha</p><p><br></p>
</div><br></div></div>-----Ακολουθεί συνημμένο-----<br><br><div>-- <br>gmx-users mailing list <a href="http://mc/compose?to=gmx-users@gromacs.org" target="_blank">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>
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Please don't post (un)subscribe requests to the list. Use the<br>
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Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br>
<br>post-doctoral researcher<br>Molecular Dynamics Group<br>* Groningen Institute for Biomolecular Research and Biotechnology<br>* Zernike Institute for Advanced Materials<br>University of Groningen<br>The Netherlands<br>