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

[Shirts, Michael R. (mrs5pt)]

-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.

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.

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.