[gmx-users] clustering using gromos method

[Adriana Garro]

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