<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear Sulatha, <br><br>You can try the command <span style=""></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><mssulatha@gmail.com></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 <mssulatha@gmail.com><br>Θέμα: [gmx-users] micelle clustering<br>Προς: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Ημερομηνία: Πέμπτη, 30 Ιούνιος 2011, 9:18<br><br><div id="yiv1715537234"><style>
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<p class="yiv1715537234MsoNormal">Hi all,<br></p><p class="yiv1715537234MsoNormal">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 style=""> </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" target="_blank" href="http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering">http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering</a></pre>
<p class="yiv1715537234MsoNormal">and also looked at the various posts given on this topic, (specifically
Chris Neale’s and Tsjerk’s mails).</p>
<p class="yiv1715537234MsoNormal">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 style=""> </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 class="yiv1715537234MsoNormal"> </p>
<p class="yiv1715537234MsoNormal">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 class="yiv1715537234MsoNormal">I tried the command 1 with </p>
<p class="yiv1715537234MsoNormal"><span style=""> </span>trjconv -f a.xtc -o
b.gro -pbc cluster -e 0.002 </p>
<p class="yiv1715537234MsoNormal">and also</p>
<p class="yiv1715537234MsoNormal"><span style=""> </span>trjconv -f a.xtc -o
b.gro -pbc cluster –dump X (where x=2, 4, 6, 8 etc..)</p>
<p class="yiv1715537234MsoNormal">The program gets into a never ending loop. </p>
<p class="yiv1715537234MsoNormal">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 class="yiv1715537234MsoNormal">I will greatly appreciate any help on how to go about doing
this specifically which frame (for dump or –e argument) .<span style=""> </span>Please guide me on this.</p>
<p class="yiv1715537234MsoNormal">I also downloaded the modified trjconv.c<span style=""> </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 class="yiv1715537234MsoNormal"><br></p><p class="yiv1715537234MsoNormal">Thanks for any help or clue,<br></p><p class="yiv1715537234MsoNormal">Sulatha</p><p class="yiv1715537234MsoNormal"><br></p>
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