[gmx-users] clustering using gromos method

XAvier Periole x.periole at rug.nl
Mon Jan 12 17:12:20 CET 2015

with the gromos method the criteria is the RMSD between the structure of the objects given to cluster …. two neighbours are two structures that are within this cutoff (eg. 0.25) 

obviously defining an RMSD between the two objects should make sense.

On Jan 12, 2015, at 4:56 PM, Adriana Garro <adrianagarrosl at gmail.com> wrote:

> Dear All,
> I am working on a Coarse Grained model (Martini force field), I have a
> trajectory file and
> I am trying to do a clustering procedure using the gromos method, this is
> the command line I used
> g_cluster -f dynamic.xtc -s dynamic.tpr -o cluster.xpm -clid
> cluster-id-over-time.xvg -cl clusters.pdb -cutoff 0.25 -method gromos -skip
> 10
> and it finished well, I got more than 40 clusters, of course if I vary the
> cutoff this number changes but I am not sure what is the more optimal value
> for my system. In fact I dont understand very well what is the meaning of
> this parameter.
> I have read this
> "gromos: use algorithm as described in Daura et al. (Angew. Chem. Int. Ed.
> *1999*, 38, pp 236-240). Count number of neighbors using cut-off, take
> structure with largest number of *neighbors* with all its neighbors as
> cluster and eliminate it from the pool of clusters. Repeat for remaining
> structures in pool."
> But still...what neighbors means in this context?
> If someone can clarify this for me, I'd really appreciate it. (I cant acces
> to the original publication).
> Thanks in advance.
> Adriana
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