<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">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>To quantify this micelle clusterization, I tried to use the suggestions present in the gromacs documentations:</div><div> http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering</div><div><br></div><div>i.e </div><div> </div><span class="Apple-style-span" style="font-family: Verdana, sans-serif; font-size: 14px; "><ol><li style="line-height: 1.25; ">use <code><a rel="internal" 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; ">use <a rel="internal" 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; ">use <code><a rel="internal" 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="internal" href="http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv" style="color: rgb(0, 84, 166); ">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="internal" href="http://www.gromacs.org/Documentation/Gromacs_Utilities/grompp" style="color: rgb(0, 84, 166); ">grompp</a> -f a.mdp -c a_cluster.gro -o a_cluster.tpr</code></li><li style="line-height: 1.25; "><code><a rel="internal" href="http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv" style="color: rgb(0, 84, 166); ">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;">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.</span></font></div><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;">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;"><br></span></font></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="line-height: 17px;">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;"><br></span></font></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="line-height: 17px;">Jagannath</span></font></div></span></div></td></tr></table><br>