Biasing potential of a Metadynamics Simulation

From: Fidan Sumbul (
Date: Tue Oct 27 2015 - 13:05:02 CDT

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

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