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

[Mark Abraham]

Hi,

Yeah, we should plan for a world where mdrun doesn't write any text files,
and perhaps as few files as possible. An analysis tool that just dumps to
xvg seems like the right way to serve any need to support existing tools
that read such xvg, like gmx traj does now.

Mark

On Thu, 5 Jan 2017 16:20 David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> On 05/01/17 11:59, Berk Hess wrote:
> > We anyhow want the edr storage, since that uses an order of magnitude
> > less space.
> >
> Ok, then I will try to generate a test case for this code too.
>
> > Berk
> >
> > On 2017-01-04 16:56, Michael R Shirts wrote:
> >> 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.
> >>
> >> Best,
> >> ~~~~~~~~~~~~~~~~
> >> Michael Shirts
> >> Associate Professor
> >> michael.shirts at colorado.edu
> >> http://www.colorado.edu/lab/shirtsgroup/
> >> 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:
> >>
> >>      Hi,
> >>           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.
> >>           Cheers,
> >>           Berk
> >>           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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> >
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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