Mark Abraham





02:12 PM GROMACS Revision 5ae5bf42: Refactor SD update
The former use of multiple boolean control variables made the logic
hard to follow. Without constraints, the two part...
09:11 AM GROMACS Bug #2485: pull with cylinder geometry
Alex Smolyanitsky wrote:
> I am suppressing warnings that are completely harmless -- we messed with the ff files in ...


04:39 PM GROMACS Bug #2485: pull with cylinder geometry
Can we check for that in grompp?


12:14 AM GROMACS Bug #2485: pull with cylinder geometry
If you can, sharing also your inputs to grompp might be useful for observing that it does indeed behave well under ot...
12:04 AM GROMACS Bug #2374: GPU detection claims fallback despite this clashing with command line user request
Targeting 2018.2, assuming this is still an issue we should fix.


06:37 PM GROMACS Bug #2482: Atoms/molecules in freezegrps move and system crashes
@gmx check -s1 200ns-NVT-Eq-Gromacs5.1.4.tpr -s2 200ns-NVT-Eq-from-200ns.tpr@ suggests there are meaningful differenc...
05:53 PM GROMACS Revision 13fed60d: Introduce gmx_used_in_debug
Sometimes variables are only used to support assertions or other debug
code. This alternative annotation makes clear ...


04:52 PM GROMACS Task #2481 (New): gmx check -m writes latex methods section, but has not been kept up to date
If someone wants to adopt this, it does sound like a useful thing so that GROMACS users can generate templated text f...
10:03 AM GROMACS Revision e9a53455: Shift per-step control logic to do_md
There are multiple reasons why do_md can decide this is the last step,
so we should be consistent about it.
Refs #17...
10:03 AM GROMACS Revision acc3940a: Break apart update_constraints
There are four distinct kinds of work being done, and never was any
call to update_constraints doing all of them, so ...

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