[gmx-users] g_clustsize and monomers

David van der Spoel spoel at xray.bmc.uu.se
Sun Mar 27 21:55:10 CEST 2011

On 2011-03-27 21.27, devicerandom wrote:
> 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.
try the xpm files, and process those with xpm2ps

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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