Michael Shirts

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  • Last connection: 09/23/2018





06:34 AM GROMACS Task #1868: implement mdrun -rerun better, simplifying do_md
> Maybe just don't report the virial unless explicitly requested (with an error if not possible). Preserving old beha...


04:04 AM GROMACS Task #2616: Model for MD state
> Where do we already already need copies of state objects (such as t_state in minimize)? And are there exceptions ei...


10:29 PM GROMACS Bug #2264: Changes in bonded interactions are not considered in expanded ensemble simulations
So, I believe there may be an error here (there are lots of different ways of doing the settings that have not all be...


01:45 PM GROMACS Bug #2264: Changes in bonded interactions are not considered in expanded ensemble simulations
Berk Hess wrote:
> I voted -1 on the fix on gerrit because the group scheme non-bonded potentials are treated with i...


06:35 PM GROMACS Bug #2244: Test rerun with FEP
Berk, could you post a sample file that cause the problem? I'd love to get a regression test in the free energy sect...


09:24 PM GROMACS Feature #2186 (New): Potential change for logical improvements: move control of constraints purely to the .mdp
Here's a suggestion that could control flow control within the program logic, though it might not be worth doing beca...


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...


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 ...


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...

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