[gmx-developers] -dhdl flag in gmx energy obsolete?

Michael R Shirts Michael.Shirts at Colorado.EDU
Wed Jan 4 16:56:51 CET 2017

The reason the mechanism of storing the information necessary for recreating the .dhdl file in the .edr file was introduced was, I believe, to move away from having a separate dhdl.xvg file, and instead have that data stored in the .edr like the other energy data.  

It does seem a bit redundant to have two ways of storing and regenerating that information, but if we had to pick one, it would presumably be the .edr file to match the other methods.

Michael Shirts
Associate Professor
michael.shirts at colorado.edu
Phone: (303) 735-7860
Office: JSCBB C123
Department of Chemical and Biological Engineering
University of Colorado Boulder

On 1/3/17, 6:37 AM, "gromacs.org_gmx-developers-bounces at maillist.sys.kth.se on behalf of Berk Hess" <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se on behalf of hess at kth.se> wrote:

    I would think this is quite useful if you want to process dH/dl data 
    with something else than gmx energy, e.g. python scripts for MBAR.
    On 2016-12-29 11:16, David van der Spoel wrote:
    > Hi,
    > I am trying to find out if anyone uses the gmx energy -dhdl code 
    > pathway. The information is (typically?) read by gmx bar, but gmx 
    > energy has code to deal with this too. I could not find any queries on 
    > the mailing list, which suggests no one uses this.
    > The reason I am asking is that in my energy file analysis patch 
    > https://gerrit.gromacs.org/#/c/4310/ I preserved the code but there is 
    > no testing yet. Alternative to throwing out the code would be if 
    > someone could provide/suggest a test set.
    > Cheers,
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