[gmx-developers] -dhdl flag in gmx energy obsolete?
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jan 6 22:01:18 CET 2017
On 05/01/17 17:22, Michael R Shirts wrote:
> I added a redmine feature for this
> (http://redmine.gromacs.org/issues/2097), at low priority, so it’s
> remembered.
Great, I did implement a test for it now, hope we can finalize this soon...
>
>
>
> Best,
>
> ~~~~~~~~~~~~~~~~
>
> Michael Shirts
>
> Associate Professor
>
> michael.shirts at colorado.edu <mailto: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
>
>
>
> *From: *<gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> on
> behalf of Mark Abraham <mark.j.abraham at gmail.com>
> *Reply-To: *"gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
> *Date: *Thursday, January 5, 2017 at 9:12 AM
> *To: *"gmx-developers at gromacs.org" <gmx-developers at gromacs.org>,
> "gromacs.org_gmx-developers at maillist.sys.kth.se"
> <gromacs.org_gmx-developers at maillist.sys.kth.se>
> *Subject: *Re: [gmx-developers] -dhdl flag in gmx energy obsolete?
>
>
>
> 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
> <mailto: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 <mailto: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
> <mailto: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
> <mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> on
> >> behalf of hess at kth.se <mailto: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 <mailto:spoel at xray.bmc.uu.se>
> http://folding.bmc.uu.se
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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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