GROMACS development

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...

03/24/2019

09:44 PM GROMACS Bug #2902: 2019.1 equilibration issue? (Intel 2018u3)

Hi Stefan,
Can you try to run "make check" (ideally with all the regressiontests enabled too)? That might be able ...

03/23/2019

03:00 PM GROMACS Feature #2901: Declare external Resources in mdp / tpr files.

Commenting here instead to avoid creating noise in Gerrit!
I thought a little bit more about it over lunch, and th...

03/05/2019

04:43 PM GROMACS Bug #2876: 2019.1 make check fails on AVX and AVX2 (Intel 2018u3)

These look very benign, so it's likely just a matter of allowing a bit more freedom in the tests for the Intel compiler.