GROMACS development

03/23/2020

02:50 PM GROMACS Bug #3448: GMX 2020.1 - Multidir simulations can stop at different times when killed by job manager

Yes, my fix should have fix this for communicating code.
As PLUMED does not use an API with GROMACS, mdrun can't kno...

03/20/2020

04:20 PM GROMACS Bug #3440: Multi-nodes run exits with error with openmpi/4.0.0

Which MPI version was GROMACS built with (I think this is written in the log file)? You can't freely mix MPI versions...

12:41 PM GROMACS Revision 655ab507: Rename class Grid to BiasGrid in AWH module

Since we do not use namespaces in modules, classes should not
use generic names, also not inside modules as that can ...

03/19/2020

11:32 PM GROMACS Bug #3403: solvation free energy with couple-intramol set to no

What do you mean with adding long-range interactions for those pairs?
Note that table-extension does nothing in re...

10:14 AM GROMACS Revision 9519d4cf: Simplify finish_update()

Now that coordinates are no longer shifted using the graph
in do_force() and not shifted back in finish_update(),
the...

09:50 AM GROMACS Revision 9dce7177: Remove at_start from t_graph

The start atom for shifting was always 0, so no longer needed.
Also improved the naming of several variables.
Change...

03/18/2020

11:15 PM GROMACS Bug #3441 (Resolved): Ewald surface-epsilon is incorrect

Applied in changeset commit:2548c9e0ce93d295e10d953f10763f7700ea7d17.

11:05 PM GROMACS Revision ecf42f0e: Remove use of graph in do_force()

Removed all unused code paths using t_graph.
TODO: Remove the double coordinate copy in the update code.
Change-Id:...

11:04 PM GROMACS Revision 2548c9e0: Use WholeMoleculeTransform for orires and epsilon-surface

Remove direct use of the graph from the orientation restraint
and Ewald epsilon-surface term code by passing in whole...

11:04 PM GROMACS Revision a7dc278e: Add WholeMoleculeTransform class

This class manages a coordinate buffer with molecules not split
over periodic boundary conditions for use in force ca...