GROMACS development

12/10/2020

09:30 AM GROMACS Revision df3107de: Improved variable names in FEP nonbonded kernel

This is mainly to improve the readability of the FEP SIMD patch.
There are more variables to rename, but preferably a...

12/04/2020

09:47 AM GROMACS Revision 201eb7db: Added scalar functions cbrt as well as masked Rcp

These functions as useful for nonbonded FE SIMD kernels.

11/23/2020

07:48 PM GROMACS Revision e10c7a35: Properly check if there are perturbed constraints or masses

Instead of just checking, when running updates on GPU, if
there are lambda states that involve constraints or masses
...

11/05/2020

09:39 AM GROMACS Revision 3b823056: Set pbcatom_input in order to pass later checks

pbcatom_input was not set. This meant that pbcatom checks in
set_pull_init() failed for large pull groups.
Fixes: #3786

11/03/2020

10:05 AM GROMACS Revision afac7a2e: Remove TODO regarding AWH cover threshold along lambda axis.

The 1.0 factor should be OK for a FEP lambda axis. It should be OK
in theory and tests show it works.
Change-Id: Iaf...

10/16/2020

01:58 PM GROMACS Revision 9c157fac: When loading AWH user data do not convolve the bias along FEP dims.

Fixes: #3736.

10/09/2020

08:25 AM GROMACS Revision 62fd07ed: AWH: Remove random term from FEP tests

Test if it is the random numbers that are making tests fail on
some builds.
Fixes: #3660
Change-Id: I3e189d7770f0089...

09/21/2020

11:07 AM GROMACS Revision 054bf288: AWH avoid constructors only differing in parameter types

Also clarified a function name in the tests.
Tests had to be updated since the force constant (now removed)
should no...

09/03/2020

01:35 PM GROMACS Revision 7d7cbb84: Print lambda state to log file if using AWH for FEP.

Change-Id: I08c7e6d51a299eb53556d5bde63c29f7c7640f6e

08/25/2020

03:01 PM GROMACS Revision 87516a80: Avoid log(0) if probability is too low

Change-Id: I96f5aa61f21303c4c382b8a0664cffd20e85bbd6