[gmx-users] problem with trjconv -pbc cluster

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Jul 7 18:56:21 CEST 2010

I wrote my own program to do this and so I never tried that one. We  
did find that clustering based on a dingle atom in the chain was a  
very good idea. So take your distal carbon in the surfactant and make  
in index group of it and cluster it (with a larger cutoff) with  

Obviously if there is a problem with g_clustsize then you should also  
file a bugzilla.

If you're going to continue with this thread about g_clustsize, then  
please pick an appropriate subject line so that others can search it  
usefully later.


-- original message --

Hi Chris,  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. 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.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.
Here is the command line I used:   g_clustsize -f traj.xtc -s topol  
-mol -cut 0.50 I used -mol option so that I get the cluster size  
distribution in terms of the molecules.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)Besides, at any other time, the maximum size of  
particles predicted by g_clustsize does not match with what VMD shows.  
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.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.   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.So, do you have any suggestions ? Any help  
in pointing out where I am doing wrong will be helpful.Jagannath

--- On Wed, 7/7/10, chris.neale at utoronto.ca <chris.neale at  
utoronto.ca> wrote:

From: chris.neale at utoronto.ca <chris.neale at utoronto.ca>
Subject: [gmx-users] problem with trjconv -pbc cluster
To: gmx-users at gromacs.org
Date: Wednesday, 7 July, 2010, 9:27 PM

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