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

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 6 11:49:21 CEST 2015

On 05/10/15 22:02, Shirts, Michael R. (mrs5pt) wrote:
>> Correct, -odh. Sorry about the mixup.
>> So this is useful?
>> In that case I can fix it up and make it work.
> There is a bit of redundancy there. There are two ways to run free energy
> calculations -- put the data to a plaintext file, and put it into the
> .edr.  -odh is necessary to put it into the edr.  If the information is
> already being put into the .edr, it's probably worth it to retain the
> ability to take it back out - otherwise, there's a lot of complexity being
> carried around in the .edr with no usage.  It is lower storage to put the
> information in the .edr.  The information does need to be in the .edr for
> gbar to work right now.
In fact the present gmx energy has no option to generate an edr file so 
now I am confused!

However I am not touching the edr files, so no worries there.

>> Indeed -fee. This is not something we want to encourage ("The free
>> energy difference was computed using GROMACS.").
> Yes, kill it with fire.

> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Associate Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434) 243-1821

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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