From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Thu Feb 03 2011 - 10:49:22 CST
Hi Alexandra, sorry: the guide is clearly inaccurate at that point. We
should have mentioned there, that there is currently no support for summing
together dihedral angles, because of their periodicity. I can tell you
where to disable the error message, but whenever one of your dihedrals jumps
in value from +180° to -180°, your average dihedral will also change by
360°/6 = 60°. It is already troublesome to analyze, but forget about
applying forces for now. There isn't yet in the code the possibility to sum
dihedrals in a correct way (using e.g. Cartesian coordinates on a circle),
but I will let you know when we'll insert this feature into the code.
What type of forces would you like to apply to this average dihedral? Is
there any way that the simulation may be set up in an equivalent way that
doesn't involve summing together dihedrals?
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
---- ----
On Thu, Feb 3, 2011 at 2:30 AM, Alexandra Nemkevich <
20407619_at_student.uwa.edu.au> wrote:
> I am trying to set up a colvar that is an average of six dihedral angles--90e6ba4fc184fcd864049b638d3b--
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