GROMACS development

11/21/2018

10:41 PM GROMACS Bug #2754: Simulated Tempering seems to be broken

Michael: What was the result of your testing last week?

10:30 PM GROMACS Task #2770: change branch maintenance policy

Reading up in detail on the tools we use, studying the config files used, and then documenting that properly for othe...

06:50 PM GROMACS Task #2770: change branch maintenance policy

Yeah, but merging to master usually doesn't have any deadline/urgency.
I'll look into moving some stuff during the...

04:33 PM GROMACS Task #2770: change branch maintenance policy

I think what we failed to consider last year is the 2-3 month period that happens after branching off the new release...

11/20/2018

05:19 PM GROMACS Task #2771: Size independent Hessian for normal mode analysis

David van der Spoel wrote:
> h = sqrt(eps) * std::max(fabs(x), 0.001)
No, the spacing for the 2-point approxima...

02:52 PM GROMACS Task #2771: Size independent Hessian for normal mode analysis

This problem is actually quite a bit harder than it might appear at first sight, and has to do with the fundamental p...

11/15/2018

04:56 PM GROMACS Bug #2757: mdrun refuses to start with .cpt if nsteps is -1 in .tpr

While Paul's change might fix the acute problem, it adds to the already complex checking related to restarts. Not at ...

11/06/2018

12:57 PM GROMACS Bug #2719: PME broken with Intel OpenCL on OSX

Apple has merely announced that it will be deprecated a year from now.
This case is old hardware, but given that i...

11/02/2018

05:12 AM GROMACS Bug #2719: PME broken with Intel OpenCL on OSX

Yes, this is on OS X.
As Mark says, it's not an important feature to have, but we should just make sure to disable...

10/30/2018

09:02 AM GROMACS Bug #2642: mdrun with SIMD triggers floating point exceptions

Hi,
Sorry if I'm storming in and providing thoughts you have already considered, but in that case you can just ign...