[gmx-users] AWH with two bias potentials

Berk Hess gmx3 at hotmail.com
Thu Feb 14 17:41:31 CET 2019

I see now that you used awh-nbias=2 with awh-ndim=1. Thus you asked for 2 independent 1D AWH  biases and PMFs. You might be able to get a 2D PMF from that, but that is complicated.
I think that what you want is one 2D bias: awh-nbias=1 with awh-ndim=2.


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Cédric Leyrat <Cedric.Leyrat at igf.cnrs.fr>
Sent: Thursday, February 14, 2019 4:32 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] AWH with two bias potentials

Dear Berk,

I do get a set of PMF files at different times for each reaction
coordinate from gmx awh. Each file has two columns (x=coordinate 1,
y=PMF or x=coordinate 2, y=PMF). My coding and maths skills are quite
limited so if you have a script that can convert these data to a 2D
format, I would be happy to use it.


Le 2/14/2019 à 3:27 PM, Berk Hess a écrit :
> gmx awh writes out the 2D (or any-D) PMF to xvg files for different times. The 1D nature of xvg files is not convenient for visualization though, so you need to write a script to convert it to you favorite 2D data format. I probably have a script somewhere for some 2D format (python?) if you can't write it yourself.
> Berk
Cédric LEYRAT, Ph.D
Chargé de recherche - INSERM
Institut de Génomique Fonctionnelle
141, rue de la cardonille
34094 Montpellier Cedex 05 - France
tel: +33 (0)434359272

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