Re: Question about PMF calculation

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Jun 25 2019 - 11:14:19 CDT

Hello Parinaz, since this is a general question it should be sent to the
mailing list (I assume you used NAMD based on your previous emails).

For metadynamics and ABF, a .pmf file is written with contents
self-explanatory. If you enabled writeTIPMF for a harmonic restraint or
metadynamics, the file would be .ti.pmf. All other methods give you
quantities that require post-processing: the details depend on which method
you used, which you did not specify in your question.

Giacomo

On Tue, Jun 25, 2019 at 11:39 AM parinaz bashirbanaem <
parinaz.bashirbanaem_at_gmail.com> wrote:

> Dear Professor Fiorin,
>
> I reduced the distance of two atoms in a few steps, so that in each step
> after reduction, done equilibration. I want to calculate PMF using NAMD
> colvar package. How can I extract PMF from those runs? Thanks in advance.
>
> Best regards.
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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