<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><span class="Apple-style-span" style="font-family: 'times new roman', 'new york', times, serif; font-size: 16px; "><div>Hi Chris,</div><div> Thanks a lot for your responses. I will surely try them. But, before I go to trjconv -pbc cluster, I had one more problem to sort out. This has to do with quantifying the cluster-size distribution from the trajectory. </div><div>As I mentioned, if I visualize the trajectory in VMD, I see that starting from a random dispersed state of 50 molecules of surfactant, it aggregates gradually and at a long time, two distinct miceller aggregates are formed.</div><div>But, If I try to quantify the cluster-size distribution using g_clustsize utilty, it gives me bizarre results: the maxclust.xvg for the final time frame shows that I have 1 single cluster containing all the 50 molecules. But, Vmd shows 2 distinct
aggregate.</div><div><br></div><div>Here is the command line I used:</div><div> g_clustsize -f traj.xtc -s topol -mol -cut 0.50 </div><div>I used -mol option so that I get the cluster size distribution in terms of the molecules.</div><div>Here, executing the commands gives me maxclust.xvg which has maximum size of clusters( in terms of molecule number) as a function of time frame. It shows at the end, maxclustersize is 50 and it has all the particles in it( as obtained from maxclust.ndx)</div><div>Besides, at any other time, the maximum size of particles predicted by g_clustsize does not match with what VMD shows. </div><div>I also tried post-processing the trajectory using trjconv with -pbc whole or with -pbc nojump . But, g_clustsize always returns same result:maxcluster contains all the particles.</div><div>Then I tried playing with -cut option : I started with default value of 0.35, here the result is worse: it
shows maxclust = 1 i.e all the particles are monomeric . But any value beyond 0.35 gives me maxclust = 50. </div><div> </div><div>I tried to cross-check whether visualization is misrepresented or not: for this I tried to calculate all the distances among the com of the surfectants using g_dist tool and tried to manually cluster the surfectants and I found that here I can easily come up with two separate cluster based on the distances. So, I think that the problem lies in g_clustsize not in visualization, as -pbc whole or -pbc nojump does not change the result.</div><div>So, do you have any suggestions ? Any help in pointing out where I am doing wrong will be helpful.</div><div>Jagannath</div><div><br></div></span><br>--- On <b>Wed, 7/7/10, chris.neale@utoronto.ca <i><chris.neale@utoronto.ca></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From:
chris.neale@utoronto.ca <chris.neale@utoronto.ca><br>Subject: [gmx-users] problem with trjconv -pbc cluster<br>To: gmx-users@gromacs.org<br>Date: Wednesday, 7 July, 2010, 9:27 PM<br><br><div class="plainMail">PS:<br><br>you realize that trjconv -pbc cluster is never going to work unless you actually have a cluster, right? So you can't start this procedure near your initial dispersed state. You need to start at some time T where you actually do have a cluster. Then you can try -dump T, -dump (T+X), -dump (T+X*2), etc. Then you can follow the ides expressed below like running backwards with -pbc nojup to get the initial state.<br><br>Chris.<br><br>--original message --<br><br>Dear Jagannath:<br><br>There is, as far as I know, no way to fix this. Here's what you should do.<br><br>1. Let the space between your timesteps be X ps.<br>2. Use trjconv -pbc cluster -dump X -o out.gro<br>2b. if that doesn't work, try trjconv -pbc cluster -dump (X*2) -o
out.gro<br>2c. if that doesn't work, try trjconv -pbc cluster -dump (X*3) -o out.gro<br>...<br>(Note use real numbers for args to -dump).<br><br>Once you have a frame that works, you can run part 2 and 3 of that<br>wiki page by making a tpr based on the gro that worked -- and I think<br>that you'll need to run your trjconv -pbc mol starting from the frame<br>where clustering worked (e.g. -b X). Note that this second requirement<br>means that you may need to reverse the frames from your .xtc file so<br>that you can run in reverse time from a complete micelle through to<br>disassembly with -pbc nojump -- a for loop around trjconv will work<br>but inefficiently, you might be able to use -demux smartly here (I'm<br>not sure).<br><br>But then since you have 2 micelles you will need a starting box in<br>which they are both whole.... getting trickier. You should be aware<br>that the trjconv -pbc cluster is not the only way to do part 1 from<br>that wiki page.
You could use trjconv -trans X Y Z and then make a new<br>.tpr and then run trjconv -pbc nojump and it would work if only you<br>knew which X Y Z to use (although trial and error may help you here<br>eventually).<br><br>Sorry this is confusing, but this is a difficult thing to do and you<br>should expect to struggle with it for some time, so another questino<br>to ask yourself is "do I really need to do this?" If its just for<br>making a movie then you can use pbctools in vmd for that.<br><br><br>Chris.<br><br>-- original message --<br><br>Hi, I had a system of surfectants which are started with an initial<br>configuration where all of them are well dispersed. Visual study of<br>trajectory shows they start aggregating and finally form two discrete<br>micelles. To quantify this micelle clusterization, I tried to use the<br>suggestions present in the gromacs documentations:<br><a href="http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering"
target="_blank">http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering</a><br>i.e use trjconv -pbc cluster to obtain a single frame that has all<br>of the lipids in the unit cell. This must be the first frame of your<br>trajectory. A similar frame from some previous timepoint will not<br>work.use grompp to make a new tpr file based on the frame that was<br>output from the step above.use trjconv -pbc nojump to produce the<br>desired trajectory using the newly produced tpr file.trjconv -f a.xtc<br>-o a_cluster.gro -e 0.001 -pbc clustergrompp -f a.mdp -c a_cluster.gro<br>-o a_cluster.tprtrjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr<br>-pbc nojump<br>But, The first step i.e. trjconv -pbc cluster does not work. Looks<br>like it is going through an infinite loop and is not stopping for<br>convergence.<br>I am using gromacs 4.0.7<br>Any help will be appreciated.<br>Jagannath<br><br><br><br><br>--<br>gmx-users mailing list
<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">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>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></div></blockquote></td></tr></table><br>