GROMACS development

01/20/2020

02:31 PM GROMACS Task #3306 (New): Document gmx dos tool more clearly

#request
Users on the mailing list stumble regularly over the dos tool and do not know what the output means, spe...

01/17/2020

02:40 PM GROMACS Task #3076: Selectively activate MdModules during simulation instead of instantiating all of them

Selective activation of the modules is easier when MdModules don't have to be constructed with the notifications earl...

01/09/2020

03:18 PM GROMACS Task #3287 (New): Deprecate make_ndx, use select instead

We have two tools that perform very similar tasks, make_ndx and select.
gmx select is a superset of make_ndx in a...

01/08/2020

04:50 PM GROMACS Bug #3284 (New): gmx msd cannot output two xvg files as suggested by command line option

#request to fix msd xvg output behaviour
When using -mol and -o in gmx msd simulatneously, only the xvg files re...

12/20/2019

01:16 PM GROMACS Task #3260 (New): keep up to with mdspan reference implementation

To represent multidimensional data, we use mdspan that is proposed C++ extension p0009 (http://www.open-std.org/jtc1/...

01:03 PM GROMACS Task #2281: Represent data on regularly spaced N-dimensional grids.

Yes, though we would like to keep up to date with mdspan developments
I'll open a new task for this, so that this ...

12/17/2019

12:24 PM GROMACS Bug #3246: GPU code misses settle error check, simulation crashes with segfault without any further output

The issue here is that it just crashes out without any information, whereas for example in GROMACS2018.6 I get
st...

10:57 AM GROMACS Bug #3246 (Accepted): GPU code misses settle error check, simulation crashes with segfault without any further output

Running the 216 SPC water box on a single GPU with cut-off electrostatics segfaults without any other warning.
Fin...

10:42 AM GROMACS Bug #3245 (Closed): Continuing mdrun from checkpoint, gromacs refuses appending despite present files

10:20 AM GROMACS Bug #3245 (Closed): Continuing mdrun from checkpoint, gromacs refuses appending despite present files

When asking to append to existing files after continuing mdrun from a checkpoint, appending is refused on the grounds...