[gmx-users] clustering using gromos method

[Adriana Garro]

Thanks for the reply Xavier.
Cheers,

Adriana

***********************************************************
Dra. Adriana D. Garro
Química Medicinal
Facultad de Química, Bioquímica y Farmacia
Universidad Nacional de San Luis
IMASL-CONICET
San Luis, Argentina

Tel..............:+54 266 4424689  int 6153
e-mail...: adgarro at unsl.edu.ar
e-mail...:  adrianagarrosl at gmail.com


**********************************************************

2015-01-12 17:12 GMT+01:00 XAvier Periole <x.periole at rug.nl>:

>
> 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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