[gmx-users] g_clustsize and monomers

[devicerandom]

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 
fault).

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 
aggregates).

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

-- 
http://devicerandom.org