Re: Colvar with variable axis

From: Giacomo Fiorin (
Date: Thu Mar 12 2015 - 06:23:31 CDT

Please check the documentation of distanceZ, and ref2 in particular. If
that doesn't work for you, please check refPositionsGroup as well.

On Thu, Mar 12, 2015 at 12:01 PM, Mitchell Gleed <>

> Hello,
> 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.
> Mitch

Giacomo Fiorin
Assistant Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213

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