Re: clustering

[Nicholas M. Glykos]

> 1) Is carma clustering method base on RMSD?

https://arxiv.org/abs/1512.04024



> 2) after performing the clustering command, I had 4 clusters in my
> trajectory. How could I find the representative of each cluster?

Use grcarma (instead of carma). It will automatically produce
representative structures for each cluster.

https://github.com/pkoukos/grcarma



> 3) What is the relationship between the DG files and and clusters? If we
> have 2 plots (the clusters in the PCA1-PCA2 space and the DG values in the
> PCA1-PCA2 space), are both plots correspond to each other? I mean, how could
> we find the energy of each point of clusters in the DG diagram? (find the
> attachments)


https://utopia.duth.gr/glykos/carma.html#section_81
https://utopia.duth.gr/glykos/carma.html#section_80

You can get the ΔG values from the header of the postscript files, or you
can use grcarma (which explicitly prints these values).



--


Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, https://utopia.duth.gr/glykos/