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

Shirts, Michael R. (mrs5pt) mrs5pt at eservices.virginia.edu
Mon Oct 5 18:21:56 CEST 2015

-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

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.

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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