GROMACS development

12/20/2019

01:29 PM GROMACS Revision 37516546: Remove problematic output of gmx angle

It could happen that the calculation of the standard deviation
for angles caused a divide by zero error for empty pop...

12/15/2019

02:15 PM GROMACS Bug #3230 (Resolved): mdrun-test -ntmpi 2 deadlock in calculateForces in density fitting

Applied in changeset commit:11395f380d11986299e230bb0c0504cf726a0f4b.

02:03 PM GROMACS Revision 11395f38: Fix densityfitting stalling and energies

Density guided simulations would stall when there were no atoms on a
node. Further, the energy contributions were add...

12/12/2019

03:49 PM GROMACS Revision 41b79d8a: Densityfitting - enforce similarity increase with adaptive force scaling

Previous to this patch, the force constant for density guided
simulations with adaptive force constant scaling was sc...

12/06/2019

12:48 PM GROMACS Revision b09c6e12: Change arbitrary units to counts in RMSD distance distribution output

Users were confused by the "a.u." label in the RMSD distance
distribution output. This patch changes the label to "co...

12/05/2019

09:00 AM GROMACS Revision a83b3bdd: Relax cross-correlation test precision

Relase the floating point precision in cross-correlation evaluations on
large data arrays further. i386 fails here wi...

12/04/2019

02:45 PM GROMACS Revision 7732ebb4: Remove cutoff-scheme group from default mdout.mdp output

The .mdp default output file had a reference to the group scheme in it,
which might prove confusing to users that ass...

12/02/2019

02:52 PM GROMACS Revision 245b4433: Relax test tolerance for cross correlation measure for densities

Some compilers do not perform the optimisations that are necessary to
reach default real tolerance when calculating t...

11/28/2019

07:15 AM GROMACS Bug #3215 (Resolved): Density guided simulation does not output energy term when density-guided-simulation-nst > 1

Applied in changeset commit:309ffe7602d3d870eb30e0be2fabb4e6763b828a.

07:14 AM GROMACS Revision 309ffe76: Fix check-pointing for density guided simulations

Previously, checkpointing for density-guided simulations did not take
into account that the checkpointing occurs in t...