From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Mon Feb 14 2011 - 09:43:33 CST
Hello Asjasja, have you tried defining a dihedral, using the four atom
groups you mention? Perhaps I'm missing a small detail, but it seems to me
that it would provide you what you need, at least when you define the two
axes dynamically, based on the centers of mass of those groups.
If the difference is only adding the two axes as fixed in space (with axisand
planeAxis), based on the gradients and system forces of dihedral, either
Jérôme or I can derive fairly easily an alternate code.
Giacomo
---- ----
Dr. Giacomo Fiorin
ICMS - Institute for Computational Molecular Science - Temple University
1900 N 12 th Street, Philadelphia, PA 19122
giacomo.fiorin_at_temple.edu
---- ----
2011/2/14 Ajasja LjubetiÄ <ajasja.ljubetic_at_gmail.com>
> Dear NAMD developers,
>
> After a lot of thought I have come to the conclusion that I would really
> need to sample my system along a colvar similar to the phi component of
> polar coordinates.
> The colvar would measure the angle between the projections of a vector and
> a reference vector on a plane.
>
> A suitable name for the colvar component would be either angleProjectionor
> angleXY.
> It could except the following parameters:
>
> - main and ref to define the main (measured) vector.
> - ref2 or axis to define the reference vector
> - ref3 and ref4 or planeAxis to define the normal vector of the plane--90e6ba4fc1f4dba169049c3feafe--
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