Re: FES analysis

From: Giacomo Fiorin (
Date: Tue May 24 2016 - 16:00:51 CDT

Hi Stefano, VMD has an interface for the Colvars module:

If you have a metadynamics simulation already run with NAMD, you could load
its state file using the "cv" command, and loop over trajectory frames
while calculating the energy of the metadynamics potential. At that point,
you can use "animate goto" to display the frame with a certain free energy.

It is a relatively recent feature for VMD, try if possible to use a very
recent version, preferably compiling the CVS version of VMD:
and using the latest colvars version:
Or simply wait for VMD 1.9.3 to be out.


On Tue, May 24, 2016 at 4:46 PM, Stefano Guglielmo <> wrote:

> Dear namd users,
> maybe the question is not so smart, but I wonder whether NAMD (or
> eventually VMD) has any tools to extract coordinates of significant
> configurations from free energy surface, like the one obtained through a
> metadynamics simulation, in order to characterize energy basins.
> Any advice will be greatly appreciated.
> With regards
> Stefano.
> --
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707678

Giacomo Fiorin
Associate 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
Lab page:
*"As computer programmers we have a responsibility to make sure that we run
the computers instead of the computers running us."*  - Steve Oualline

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