[gmx-users] clustering using gromos method

[Adriana Garro]

Another question just to be sure that I get what I want.
I want the structure with the smallest average distance to the others (The
center of a cluster) for each cluster written in the clusters.pdb file
(option -cl), but after calculation I get this message in the log file


"Writing middle structure for each cluster to clusters.pdb"

 is it ok??

the command line I used
g_cluster -f dynamic.xtc -s dynamic.tpr -o cluster.xpm -minstruct 20 -sz
cluster-sizes.xvg -clid cluster-id-over-time.xvg -cl clusters.pdb -cutoff
0.3 -method gromos -skip 10 -dist rms-distribution.xvg -noav

Thanks for your time!

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


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

2015-01-13 9:46 GMT+01:00 Adriana Garro <adrianagarrosl at gmail.com>:

> 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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