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

[Michael R Shirts]

I added a redmine feature for this (http://redmine.gromacs.org/issues/2097), at low priority, so it’s remembered.

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.
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