[gmx-developers] Remove features from gmx energy -fediff and -dhdl

[David van der Spoel]

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
> codes.
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.").

> Best,
> ~~~~~~~~~~~~
> 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:
>
>> Hi,
>>
>> I've been working on an updated version of the gmx energy tool in patch
>> https://gerrit.gromacs.org/#/c/4310/55.
>>
>> Until now I have not implement properly -fediff and -dhdl since my
>> impression is that these are not used. Can they be removed?
>>
>> Cheers,
>> --
>> 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
>> --
>> Gromacs Developers mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
>> or send a mail to gmx-developers-request at gromacs.org.
>


-- 
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