Re: Biasing potential of a Metadynamics Simulation

From: Giacomo Fiorin (
Date: Tue Oct 27 2015 - 13:14:06 CDT

Fidan, the first column of the traj file is the step number, the second is
the collective variable.

There is no kinetic energy by default in metadynamics.

The email thread refers to the data found in the state file, which contains
a grid with the metadynamics energy and forces, and additional explicit
Gaussian hills when these are off-grid.


On Tue, Oct 27, 2015 at 2:05 PM, Fidan Sumbul <> wrote:

> Dear NAMD Users,
> I'm trying to perform a multiple replica well-tempered metadynamics
> simulation by using an eigenvector as bias. As a trial, I perfomed a 20ps
> run with a 300K temperature increase. The simulation completed without any
> problem. However, I would like to calculate the biasing potential during
> the simulation. I know the first column of the colvars.traj file is the
> value of the bias, but I didn't understand what is the last column
> (E_metadynamics1) is for. Is it the summation of the E_potential and
> E-kinetic of the bias?
> I found a conversation in this mailing list stating that the first list of
> data after the definition of the colvars is the biasing potential.
> My second question is, if it is so, shouldn't it be as many as the number
> of output step as in the colvars.traj file?
> I'm attaching colvars.state file and colvars.traj file.
> thank you in advance for your answers.
> --
> Fidan Sumbul
> PhD Student and T.A.
> Polymer Research Center
> Department of Chemical Engineering
> Bogazici University

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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