Hi Rebeca,
You'd need to use k-means/k-medians clustering for that, which is not in
gmx cluster. I'd suggest to perform PCA and collect the projections onto
the first ten or so eigenvectors to decrease the dimensionality. This data
matrix you can then process with, e.g., R to perform k-means clustering.
Cheers,
Tsjerk
On Mar 31, 2015 2:00 AM, Rebeca García Fandiño rega...@hotmail.com
wrote:
Dear Gromacs users,
I am trying to find a method to obtain a fixed
number of clusters (using g_cluster) from a MD simulation. The search of
clusters is very manual, depending a lot of the cutoff selected for
the analysis. Is there any way to calculate a fixed number of clusters
from a MD simulation, in such way that the program calculates the proper
cutoff to provide the exact number asked by the user?
Best wishes,
Rebeca.
Dr. Rebeca Garcia
Santiago de Compostela University
Spain
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
