[gmx-users] clusterization in dihedral space

Justin Lemkul jalemkul at vt.edu
Tue Jan 22 19:22:15 CET 2013

On 1/22/13 1:17 PM, francesco oteri wrote:
> Thank you Mark and Justin,
> do you have any reference where this kind of clustering is explained?

What clustering?  I assumed that you had a definition of what you wanted to 
define when you posed the original question.

> I mean, since i need a parameter representing the difference between two
> frames
> to build the matrix, what is the parameter I can use starting from the
> dihedrals?

Perhaps you should find a literature example of what you want to do and revisit 
Chapter 8 of the manual, then pose a more direct question.  In order to provide 
you an answer to this question, we need to know (1) what you've done, (2) what 
you're thinking of doing, and (3) what you're actually measuring.  Since we know 
none of these, it's impossible to give any sort of recommendation.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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