[gmx-users] problem with g_clustsize

[jagannath mondal]

Thanks. Just wondering what is a 'distal atom' as you mentioned. 
 I am creating a new subject on g_clustsize. 

--- 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, 10:26 PM

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 g_clustsize.

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.

Chris.

-- 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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