[gmx-developers] Remove features from gmx energy -fediff and -dhdl
David van der Spoel
spoel at xray.bmc.uu.se
Mon Oct 5 21:34:47 CEST 2015
On 05/10/15 18:16, Shirts, Michael R. (mrs5pt) wrote:
> -dhdl extracts the .dhdl file from the .edr and is a mdrun option. Do you
> mean -odh? That generates what would be printed out in the .dhdl.xvg file
> from the .edr. Hopefully this code would be fairly modular from existing
Correct, -odh. Sorry about the mixup.
So this is useful?
In that case I can fix it up and make it work.
> I don't see at -fediff. Do you mean -fee? I would be in favor of getting
> rid of it, since it's almost always a bad estimate (just doing exponential
> reweighting). The same thing can be done with a few commands fairly
> easily (rerun + a couple of lines of python) if you really want to do that.
Indeed -fee. This is not something we want to encourage ("The free
energy difference was computed using GROMACS.").
> Michael Shirts
> Associate Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434) 243-1821
> On 10/5/15, 11:48 AM, "David van der Spoel" <spoel at xray.bmc.uu.se> wrote:
>> I've been working on an updated version of the gmx energy tool in patch
>> Until now I have not implement properly -fediff and -dhdl since my
>> impression is that these are not used. Can they be removed?
>> 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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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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