GROMACS development

05/23/2017

09:24 PM GROMACS Feature #2186 (New): Potential change for logical improvements: move control of constraints purel...

Here's a suggestion that could control flow control within the program logic, though it might not be worth doing beca...

03/11/2017

08:32 AM GROMACS Feature #2137 (New): Preliminary refactoring of constraints and update machinery.

As per Mark Abraham, preliminary refactoring of the constraints or update machinery, with a view to evolving a more c...

08:30 AM GROMACS Bug #2020: Possible issue with md-vv integrator

Did this get resolved?
Regardless, bumping so I remember to look at this when we are testing the physical consi...

02/25/2017

11:21 PM GROMACS Revision 198bc2a9: Fix for an incorrect check that nstlog !=0

The original version was accidentally reversed, causing it to
fail when nstlog =/= 0. Wasn't noticed because of lack ...

02/19/2017

05:04 AM GROMACS Feature #1137: Proposal for integrator framework (do_md) in future GROMACS

> Saving output should probably be done by handing off a buffer according to the user's schedule to a thread e.g. doi...

04:29 AM GROMACS Feature #1137: Proposal for integrator framework (do_md) in future GROMACS

> Similarly, I'm not convinced there's a good role for Element::update(). Each element knows what requirements it has...

04:17 AM GROMACS Feature #1137: Proposal for integrator framework (do_md) in future GROMACS

> Integrator had a depth field - I don't think it should ever need to know.
Looking at this more, I think we can a...

03:42 AM GROMACS Feature #1137: Proposal for integrator framework (do_md) in future GROMACS

Will be responding over several comments
> I recall Michael was planning to upload an update, but I don't see it yet...

02/15/2017

06:42 AM GROMACS Feature #1137: Proposal for integrator framework (do_md) in future GROMACS

New integrator proposal to discuss during the call 2/15/2017 posted.

01/31/2017

05:13 AM GROMACS Task #1868: implement mdrun -rerun better, simplifying do_md

The only thing that I think of where velocities in rerun were important is to calculate things like transport propert...