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-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Cédric Leyrat <cedric.ley...@igf.cnrs.fr> Sent: Thursday, February 14, 2019 4:32 PM To: gromacs.org_gmx-users@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 > -- Cédric LEYRAT, Ph.D Chargé de recherche - INSERM PHARMACOLOGY AND STRUCTURAL BIOLOGY OF MEMBRANE PROTEINS Institut de Génomique Fonctionnelle U1191 INSERM 141, rue de la cardonille 34094 Montpellier Cedex 05 - France tel: +33 (0)434359272 www.researchgate.net/profile/Cedric_Leyrat<http://www.researchgate.net/profile/Cedric_Leyrat> -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.