GROMACS development

06/09/2019

01:51 PM GROMACS Revision deb9a948: More quotes

Having to prepare slides for a Gromacs workshop is
a great motivation for procrastination in the form
of adding more ...

05/16/2019

08:35 PM GROMACS Revision 80d87590: Added more quotes

Lazy Friday evening entertainment.
Change-Id: If26bd56b178510224b4c24b63124fcd413e6ee42

11:50 AM GROMACS Bug #2762: incorrect results with Ubuntu 18.04 / glibc 2.27 (?) and >20 threads

I think the key question is whether the array data is always correct and the error only occurs in the summation loop,...

04/01/2019

12:01 PM GROMACS Bug #2881: mdrun -nsteps option does not work correctly

While the fix might be reasonable for 2019, I think this is a strong indication it's time to remove it entirely from ...

11:53 AM GROMACS Bug #2862: Division by zero in restrained dihedrals

PS Nicu: I very much agree with Mark this code urgently needs proper documentation, being made stable, and proper uni...

11:51 AM GROMACS Bug #2862: Division by zero in restrained dihedrals

I had a closer look at this code, and it appears to be written in a very fragile way.
* First, sin^2(x) should NEV...

03/26/2019

11:46 PM GROMACS Task #2898: Naming common variables

Just my $0.02, but I strongly agree with the points that we should optimize variable names to aid understanding of th...

11:20 PM GROMACS Bug #2641: Possible l-bfgs improvements

Oh, the normalization will also enter for things like calculating the scalar gradient, and while the code does accoun...

04:18 PM GROMACS Bug #2641: Possible l-bfgs improvements

Whether you call something "Quasi-NR step" or search direction is really just semantics. In terms of the *line minim...

12:37 PM GROMACS Bug #2641: Possible l-bfgs improvements

Gentlemen,
Let's take a step back and work on one issue (or not) at a time and properly diagnose exactly what it i...