GROMACS development

04/05/2019

05:07 PM GROMACS Revision ffd89ba4: Fixed manual for dihedral restraints.

The equations in the manual for dihedral restraints were incorrect
and inconsistent with the code in bonded.cpp.
Cha...

03/31/2019

08:17 PM GROMACS Revision 0b25ff6b: Removed confusing gpp_atomtype functions.

For some reason there were functions to extract the massB
and chargeB from atomtypes, however atomtypes do only have
...

03/29/2019

01:37 PM GROMACS Bug #2641: Possible l-bfgs improvements

Thanks, but there are way too many unrelated changes in this file to be acceptable. We need to find just the two or t...

03/26/2019

12:54 PM GROMACS Bug #2641: Possible l-bfgs improvements

Great, this would of course be much better.
I am however not convinced by your statement in gerrit that l-bfgs wor...

11:50 AM GROMACS Bug #2641: Possible l-bfgs improvements

Thanks for pointing that out. Interestingly, this bug does not show up in single precision but it does in double prec...

03/25/2019

10:20 PM GROMACS Bug #2641: Possible l-bfgs improvements

In fact there is a test in master now, which presumable will fail.

05:55 PM GROMACS Bug #2641: Possible l-bfgs improvements

I fixed it. Do we want it in 2018 as well?

04:53 PM GROMACS Bug #2641: Possible l-bfgs improvements

Git bisect points to I54f238cedc78aadb0dad080ea3b28f001dce8d94

01:02 PM GROMACS Bug #2641: Possible l-bfgs improvements

I have reproduced the issue. The minimization works fine in 4.6 but from 5.1 it is broken. Have not tested 5.0 but wi...

02/24/2019

12:35 PM GROMACS Feature #2601: Free energy calculations, soft-core potential

The free energy kernel is also left in src/gromacs/gmxlib/nonbonded/
Has it been decided whether this is going to ch...