Colvar with variable axis

From: Mitchell Gleed (
Date: Thu Mar 12 2015 - 06:01:56 CDT


I've typically used the system Z axis (0,0,1) to represent a membrane-bound
protein channel axis and to use it for collective variables such as
distanceZ, spinAngle, etc.; but the channel axis is usually only
approximated by the system Z axis, as the tilt of the protein with respect
to Z varies somewhat during the course of a simulation. Is it possible to
implement a collective variable such as distanceZ with an axis that
continuously updates using the colvars module? I'm thinking maybe some of
the other distance colvars (distanceVec, etc.) may hold the key, but I'm
not quite sure if that's whats needed here.


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