[gmx-users] AWH with two bias potentials

Berk Hess gmx3 at hotmail.com
Thu Feb 14 20:09:27 CET 2019


Note though, as also noted in the manual, you need to be careful what you wish for. 2D biasing leads to uniform sampling of the requested rectangular area. Often you want to suppress sampling of high free-energy (unphysical or uninteresting) regions in this rectangle by using a cutoff on the free-energy.

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
Sent: Thursday, February 14, 2019 5:41 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] AWH with two bias potentials

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.

Berk

________________________________
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.

Cedric

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
>
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Cédric LEYRAT, Ph.D
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PHARMACOLOGY AND STRUCTURAL BIOLOGY OF MEMBRANE PROTEINS
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