<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Thanks for the reply. <div>I used following command to extract first frame that has all the surfectants ( as suggested by first step for characterizing micelle clustering).</div><div><br></div><div> trjconv<span class="Apple-style-span" style="font-family: monospace; font-size: 14px; line-height: 17px; "> -f a.xtc -o a_cluster.gro -dump 0 -pbc cluster</span></div><div> Here is the output I got:</div><div><span class="Apple-style-span" style="font-family: monospace; font-size: 14px; line-height: 17px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; ">COM: 0.000 0.000 19.999 iter = 19526
Isq = 12671033.000</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; ">COM: 0.000 0.000 0.000 iter = 19527 Isq = 12628369.000</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; ">COM: 0.000 0.000 19.999 iter = 19528 Isq = 12671033.000</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; line-height: 1.2em; outline-style:
none; outline-width: initial; outline-color: initial; ">COM: 0.000 0.000 0.000 iter = 19529 Isq = 12628369.000</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; ">COM: 0.000 0.000 19.999 iter = 19530 Isq = 12671033.000</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; ">COM: 0.000 0.000 0.000 iter = 19531 Isq = 12628369.000</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom:
0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; ">COM: 0.000 0.000 19.999 iter = 19532 Isq = 12671033.000</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; ">COM: 0.000 0.000 0.000 iter = 19533 Isq = 12628369.000</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; ">COM: 0.000
0.000 19.999 iter = 19534 Isq = 12671033.000</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; ">COM: 0.000 0.000 0.000 iter = 19535 Isq = 12628369.000</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; ">COM: 0.000 0.000 19.999 iter = 19536 Isq = 12671033.000</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px;
padding-left: 0px; line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; ">COM: 0.000 0.000 0.000 iter = 19537 Isq = 12628369.000</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; ">COM: 0.000 0.000 19.999 iter = 19538 Isq = 12671033.000</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px;
padding-right: 0px; padding-bottom: 0px; padding-left: 0px; line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; "><span class="Apple-style-span" style="line-height: 17px; ">looks like lsq is only fluctuating between two numbers and the program is in an infinte loop. </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; "><span class="Apple-style-span" style="line-height: 17px; "><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; "><span class="Apple-style-span" style="line-height: 17px;
">Jagannath </span></div></span></div><div><br>--- On <b>Wed, 7/7/10, Mark Abraham <i><mark.abraham@anu.edu.au></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Mark Abraham <mark.abraham@anu.edu.au><br>Subject: Re: [gmx-users] problem with trjconv -pbc cluster<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Wednesday, 7 July, 2010, 12:20 PM<br><br><div id="yiv1635627800"><br><br>----- Original Message -----<br>From: jagannath mondal <jmondal2004@yahoo.co.in><br>Date: Wednesday, July 7, 2010 16:36<br>Subject: [gmx-users] problem with trjconv -pbc cluster<br>To: gmx-users@gromacs.org<br><br><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td
style="font-family:inherit;font-style:inherit;font-variant:inherit;font-weight:inherit;font-size:inherit;line-height:inherit;font-size-adjust:inherit;font-stretch:inherit;" valign="top"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font>Hi,<div> I had a system of surfectants which are started with an initial configuration where all of them are well dispersed. Visual study of trajectory shows they start aggregating and finally form two discrete micelles. </div><div><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font>To quantify this micelle clusterization, I tried to use the suggestions present in the gromacs documentations:</div><div><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">>
</font> http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering</div><div><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font><br></div><div><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font>i.e </div><div><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font> </div><span class="Apple-style-span" style="font-family:Verdana, sans-serif;font-size:14px;"><ol><li style="line-height:1.25;"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font>use <code><a rel="nofollow" target="_blank" href="http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv" style="color:rgb(0, 84, 166);">trjconv</a> -pbc cluster</code> to obtain a single frame that has all of the
lipids in the unit cell. This must be the first frame of your trajectory. A similar frame from some previous timepoint will not work.</li><li style="line-height:1.25;"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font>use <a rel="nofollow" target="_blank" href="http://www.gromacs.org/Documentation/Gromacs_Utilities/grompp" style="color:rgb(0, 84, 166);">grompp</a> to make a new tpr file based on the frame that was output from the step above.</li><li style="line-height:1.25;"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font>use <code><a rel="nofollow" target="_blank" href="http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv" style="color:rgb(0, 84, 166);">trjconv</a> -pbc nojump</code> to produce the desired trajectory using the newly produced tpr file.</li></ol></span><div><span
class="Apple-style-span" style="font-family:Verdana, sans-serif;font-size:14px;"><ol><li style="line-height:1.25;"><code><a rel="nofollow" target="_blank" href="http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv" style="color:rgb(0, 84, 166);"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font>trjconv</a> -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster</code></li><li style="line-height:1.25;"><code><a rel="nofollow" target="_blank" href="http://www.gromacs.org/Documentation/Gromacs_Utilities/grompp" style="color:rgb(0, 84, 166);"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font>grompp</a> -f a.mdp -c a_cluster.gro -o a_cluster.tpr</code></li><li style="line-height:1.25;"><code><a rel="nofollow" target="_blank" href="http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv" style="color:rgb(0, 84,
166);"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font>trjconv</a> -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump</code></li></ol><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="line-height:17px;"><br></span></font></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="line-height:17px;"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font>But, The first step i.e. trjconv -pbc cluster does not work. Looks like it is going through an infinite loop and is not stopping for convergence.<br><br>So what command did you give, what output did you get, and does the command make sense with respect to your trajectory contents?<br><br>Mark<br><br></span></font></div><div><font class="Apple-style-span" face="monospace"><span
class="Apple-style-span" style="line-height:17px;"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font><br></span></font></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="line-height:17px;"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font>I am using gromacs 4.0.7</span></font></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="line-height:17px;"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font><br></span></font></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="line-height:17px;"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font>Any help will be
appreciated.</span></font></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="line-height:17px;"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font><br></span></font></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="line-height:17px;"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font>Jagannath</span></font></div></span></div></td></tr></tbody></table><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px;">> </font><br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search <br>> before posting!<br>> Please don't post (un)subscribe
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