<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div>Hi,</div><div> I have run a simulation using gromacs 4.0.7 with 50 copies of amphiphilic surfactant ( in water) using Martini coarse-grained force-field. Mere visualization of trajectories shows that starting with 50 discrete copies, they gradually aggregate and finally two well-separated large micelles are formed. But, my problem starts in quantifying the cluster-size-distributions . </div><div>Here is what I tried:</div><div><br></div><div>1. Initially, I was trying to directly use g_clustsize tools to calculate the cluster-size distribution. Here is the command line I used :</div><div> g_clustsize -f traj.xtc -s topol.tpr -mol </div><div><br></div><div>But, It turned out that for all the time-frame, it gives me only single cluster having
all the molecules , giving a flat line in the time-evolution of cluster-size. </div><div>This looks to be wrong as the starting configuration has all the 50 copies of surfectatnt well dispersed( at least from visualization) and at the end of the simulation the visualization shows two clusters. Here, since I am interested in the molecules that is part of a cluster , hence I used -mol option. Without this option also, I get almost all the atoms in a single cluster .</div><div><br></div><div>Then I tried </div><div> trjconv -pbc nojump -f traj.xtc -o traj_nojump.xtc </div><div> option to take care of periodicity. But, It does not change the result g_clustsize_4mpi is giving: it always gives me only 1 cluster. use of -pbc whole also gives me same result.</div><div><br></div><div>2. I also tried to play with cut-off in g_clustsize . Initially I was using default cut-off value ( 0.35 nm) . I tried
smaller value but result does not change. The most awkward part is that even if I make cut-off distance 0 as follows:</div><div> g_clustsize -f traj.xtc -cut 0.0 -s topol -mol </div><div>it still gives me a single cluster ! How can it be possible ? I am pretty sure there is something wrong but not able to figure this out. </div><div><br></div><div>3. Later, I found that in gromacs, there is a description of how to determine micelle clusters ( perhaps by Justin Lemkul ? )</div><div> Here is the steps it was recommended : </div><div> </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;">But, when I tried the first step as follows:</span></font></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="line-height: 17px;"> trjconv -f traj.xtc -o traj_cluster.gro -dump 0 -pbc cluster,</span></font></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="line-height: 17px;"> it
looks like it does not converge and enter an infinite loop: Here is an excerpt of the output:</span></font></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="line-height: 17px;"><div>COM: 0.000 0.000 19.999 iter = 19526 Isq = 12671033.000</div><div>COM: 0.000 0.000 0.000 iter = 19527 Isq = 12628369.000</div><div>COM: 0.000 0.000 19.999 iter = 19528 Isq = 12671033.000</div><div>COM: 0.000 0.000 0.000 iter = 19529 Isq = 12628369.000</div><div>COM: 0.000 0.000 19.999 iter = 19530 Isq = 12671033.000</div><div>COM: 0.000 0.000 0.000 iter = 19531 Isq = 12628369.000</div><div>COM: 0.000
0.000 19.999 iter = 19532 Isq = 12671033.000</div><div>COM: 0.000 0.000 0.000 iter = 19533 Isq = 12628369.000</div><div>COM: 0.000 0.000 19.999 iter = 19534 Isq = 12671033.000</div><div>COM: 0.000 0.000 0.000 iter = 19535 Isq = 12628369.000</div><div>COM: 0.000 0.000 19.999 iter = 19536 Isq = 12671033.000</div><div>COM: 0.000 0.000 0.000 iter = 19537 Isq = 12628369.000</div><div>COM: 0.000 0.000 19.999 iter = 19538 Isq = 12671033.000</div></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 not sure why I am getting an infinite loop ( looks like lsq is only fluctuating between two numbers). I also saw similar kind of report in the gromacs mailing list , but no proper solution came to my sight .</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; "><br></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; ">Overall, none of the attempts is giving me an appreciable result? </span></font></div><div><font
class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="line-height: 17px; ">Can someone help me on this so as to get right cluster size distribution ? 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; ">Thanks</span></font></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="line-height: 17px;">Sanku</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;"> </span></font></div></span><div style="position:fixed"></div>
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