Re: Queries regarding metadynamics and .pmf visualization

From: Giacomo Fiorin (
Date: Tue Nov 15 2016 - 10:40:15 CST

Hello Sourav, I recommend emailing the entire mailing list (of NAMD, given
your previous messages, unless you were using another simulation engine in
this case).

On Tue, Nov 15, 2016 at 1:07 AM, Sourav Ray <> wrote:

> Greetings Prof. Fiorin
> 1. I was testing the stability of a hexamer with radius of gyration and
> rmsd deviation as two coarse-grained variables.
> However, as the values of variables increase during simulation, most often
> only one or two monomers separate with rest 4/5 together in a cluster.

As you add energy through the metadynamics bias, you are probably canceling
out the associative forces between monomers.

> Please note the aggregate has no well-established database structure as
> such. My query: Is it usual for such uneven separation to occur in a
> metadynamics simulation?

It is usual: always remember that by enhancing the sampling of high
free-energy configurations, you are temporarily disrupting the stable ones.

> 2. Also, if there is any free-software that could be used in Ubuntu or
> Windows to visualize .pmf files in good quality?
> Gnuplot does the job but quality is pretty low (even with postscript) and
> Qtiplot doesn't give proper heat maps.

Gnuplot is a fully-featured plotting program with a lot of options, try
looking for those that do what you need specifically ("low quality" is a
subjective term). Matplotlib through its Python interface is also becoming
very popular. Then there are a ton of GUI-based programs, including
low-tech solutions like Excel even.

If you are using more than 1 dimension, there may be some conversion needed.

> Thanks and regards
> Sourav

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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