[gmx-users] g_clustsize and monomers

devicerandom devicerandom at gmail.com
Sun Mar 27 21:27:35 CEST 2011

On 27/03/11 16:29, David van der Spoel wrote:
> On 2011-03-27 16.42, devicerandom wrote:
>> Hi,
>> I am trying to use g_clustsize to follow aggregation of peptides. I am
>> currently using the following line:
>> g_clustsize -f my.trr -s ../my.tpr -nc nclusters.xvg -mol
>> Problem is, it actually counts monomers as clusters. I have a system
>> with 125 separate molecules, and the number of clusters starts from 125.
>> What can I do to indicate a minimum cluster size?
>> m.
> What does it matter? Just simulate longer until you get two peptides to
> aggregate. Check eg. maxclust.xvg.

Apologies, I've probably not been clear (I was writing in a rush, my 

It matters because they aggregate nicely, but I want to follow the 
number of *clusters* (that is, assemblies of 2 or more molecules) in 
time (More precisely, I want to know the number of molecules within 

Any hint? g_clustsize is a bit undocumented apart from the help page.


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