Re: Re: metadynamics run in NAMD or using plumed in NAMD

From: Giacomo Fiorin (
Date: Fri Dec 08 2017 - 07:08:36 CST

META-GUI is largely based on the use of the files COLVAR and HILLS, or
similar names. The former is named <outputName>.colvars.traj in Colvars,
the latter is called <outputName>.metadynamics.hills.traj and you can
enable it by the writeHillsTrajectory keyword.

Details are available here:


On Fri, Dec 8, 2017 at 3:06 AM, Rabeta Yeasmin <>

> Dear all,
> Thank you very much for all of your information. I am wondering if I can
> run bias-exchange metadynamics on NAMD using colvar module and how can I
> analyze results of metadynamics. In the tutorial, they had shown plotting
> pmf. But if I want to find the kinetic basins, how can I get it.
> I have found one program META-GUI for analyzing metadynamics results which
> is based on plumed output version. I am wondering if I can that program to
> analyze metadynamics from NAMD.
> Rabeta Yeasmin
> On Thu, Dec 7, 2017 at 5:49 PM, Rabeta Yeasmin <>
> wrote:
>> Dear NAMD users,
>> I am trying to run metadynamics in NAMD. I have searched online for
>> related information. I have found one tutorial in NAMD tutorial and also
>> found something like-running metadynamics using plumed version- in NAMD
>> version-. I am wondering if these two methods are same or not. If yes, how
>> am I going to use plumed with NAMD.
>> Thanks.
>> Rabeta Yeasmin

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

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