GROMACS development

03/04/2020

11:25 AM GROMACS Task #3357: Make sure "colvars" interoperates stably and smoothly with gromacs

When the MdModules are called during grompp-time, they get a chance to do the file parsing when they receive the call...

02/25/2020

11:52 AM GROMACS Feature #3374: SimulationInput abstraction

Have a look at previous discussion at "Declare external Resources in mdp / tpr files." #2901
I believe, essential ...

02/13/2020

12:04 PM GROMACS Feature #3378 (New): genion usage without stdin (facilitates use in gmx python api)

#request
Using gmx genion requires command line input to select the index group of solvent molecules.
It does ...

02/04/2020

10:30 AM GROMACS Wiki edit: Large_tasks_for_2021 (#3)

10:25 AM GROMACS Wiki edit: Large_tasks_for_2021 (#2)

02/03/2020

03:32 PM GROMACS Task #3366 (New): Enforce compability of MdModules

When MdModules modify data that is given to them they will be able to break compability to other modules that require...

01/28/2020

11:04 AM GROMACS Feature #3283: Support for the string method with swarms of trajectories in GROMACS

Just contacted the colvars authores again on what they need within gromacs and pointed to this redmine.
Created ht...

11:04 AM GROMACS Task #3357 (New): Make sure "colvars" interoperates stably and smoothly with gromacs

The Collective Variables Interface (Colvars) provides a huge number of algorithms that are based on collective variab...

01/23/2020

01:16 PM GROMACS Task #3287: Deprecate make_ndx, use select instead

There is a defselection.dat in share/top that defines default selections for the gmx select tool; It's used nowhere i...

12:00 PM GROMACS Task #3353 (New): Document gmx densmap output

#request
The output format of the gmx densmap tool is only clear after looking at the code....