Re: Defining colvars based on a region

From: Giacomo Fiorin (
Date: Mon Mar 20 2017 - 20:00:09 CDT

Not with the code currently in NAMD. Moreover, there is a difficulty in
defining a continuous function when atoms leave/center the region, so
ultimately the variable would have to be defined on all the atoms via
continuous switching functions.


On Mon, Mar 20, 2017 at 8:48 PM, Bob Faith <> wrote:

> Dear NAMD users,
> Is this possible to dynamically change the atoms subjected to a collective
> variable calculation during the simulation? For instance, is it possible to
> assign center of mass of the atoms inside a region of space as the
> collective variable since it is subjected to change at each timestep?
> Best,
> Bob

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

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