[gmx-users] g_clustsize question

David van der Spoel spoel at xray.bmc.uu.se
Wed Jul 19 19:53:56 CEST 2017

On 19/07/17 19:18, antra saxena wrote:
> Hello,
> I have a question regarding g_clustsize.
> I have a multi-peptide system and I want to determine the size of the
> cluster.
> As far as I understand, g_clustsize will cluster molecules (with -mol
> option) within each frame of a trajectory within the cutoff distance
> specified.
> With -nc option, I will get the number of clusters formed at a particular
> time of the simulation but is there a way to know how many molecules are
> part each cluster?
The -o flag will give you a colorful matrix, but it is not so useful for 
quantitative output unless you set the nlevels accurately.
>   gmx_mpi clustsize -f peptides_only.trr -tu ps -n pep.ndx -cut 0.35 -o -mol
> -s pep.tpr -pbc
> Thank,
> antra

David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.

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