[gmx-users] clustering using gromos method

[XAvier Periole]

Yes, should work.

Check that the central structures make sense. At some point this option was not giving the correct structure. 

On Jan 13, 2015, at 1:32 PM, Adriana Garro <adrianagarrosl at gmail.com> wrote:

> 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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>> 
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