From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Sun Jan 29 2017 - 10:25:38 CST
You could use distanceInv to define the minimum distance between the groups
(12 3 4) and (5 6 7 8). If that does not work for you, you can write a
similar average using a scripted function of distance components. That is,
define a colvar having as components d(1,5), d(2,6), d(3,7) and d(4,8), and
a Tcl scripted variable (
implementing this expression :
and its derivatives.
On 29 January 2017 at 00:07, The Cromicus Productions <
> 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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