Re: Modification of Colvar Module Components

From: Jérôme Hénin (
Date: Wed Oct 13 2010 - 02:24:55 CDT

Hi Alex,

>From what I understand, you just need to modify the harmonic bias
class, which is defined in colvarbias.h/colvarbias.C. The moving
restraints implemented in colvarbias.C, lines 172-219, should give you
a template. Timestep information is available as cvm::step_absolute()
(NAMD's timestep counter, including the value of firsttimestep) and
cvm::step_relative() (timestep counter within the current run).


On 12 October 2010 22:44, Alexander Predeus <> wrote:
> Hello All,
> I'm trying to implement certain modifications to colvar module that
> would allow me to use it in Hamiltonian replica exchange, with one or
> two colvars being a biased coordinate.
> I'm not an experienced programmer and figuring out relationships
> between various colvar-related classes seems quite challenging so
> far...
> Would someone (briefly) outline the strategy how can one change
> (reassign) harmonic bias force constant and/or bias center AT CERTAIN
> STEP of the simulation?
> I've done similar thing in GlobalMasterTMD successfully, but it gives
> me a lot more trouble in case of a general colvar.
> Thank you in advance,
> - Alex Predeus
> Michigan State University

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