[NAMD] Using as collective variable the minimum of a set of distances

From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Sat Jan 28 2017 - 17:07:52 CST

Hi everyone,

I'm interested in studying the separation of two strands of DNA
and to do this I want to define as collective variable
the minimum of the distances between the strands. That is,
if the DNA is
1 2 3 4
5 6 7 8
I want to define my variable as the minimum of d(1,5), d(2,6), d(3,7) and
Any idea if this is possible and how to do it?
I tried before to work with the center of mass but I don't know why
the tips of the molecule don't separate from each other.

Thanks a lot!


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