Michael Shirts
- Registered on:
- Last connection: 08/10/2019
Issues
- Assigned issues: 19
- Reported issues: 48
Projects
- GROMACS (Developer, 01/06/2011)
- Next-generation analysis tools (Developer, 05/18/2013)
- Source code reorganization (Developer, 05/18/2013)
Activity
08/12/2019
- 02:11 PM GROMACS Bug #3056: Miscalculated LJ(SR) when running with GPU?
- Mark Abraham wrote:
> Thanks for the report, the attached log files report 2018.3, so I'm changing the affected vers...
08/11/2019
- 06:39 AM GROMACS Bug #3056 (Closed): Miscalculated LJ(SR) when running with GPU?
- Collaborators in Mobley Lab found an issue where there appears to be miscalculation of the LJ(SR) with GPU. Not sure...
05/08/2019
- 08:42 AM GROMACS Feature #2944 (New): Roadmap for thermostats / barostats in new propagation/integration scheme
- We are in the process of putting thermostats and barostats into the proposed new modular integrator framework.
T...
03/05/2019
- 01:44 AM GROMACS Feature #2601: Free energy calculations, soft-core potential
- If we are talking about soft core changes. I'd also mention our essentially optimal pairwise soft core form; which co...
01/04/2019
- 06:18 PM GROMACS Bug #2824: treatment of -ndec for .gro and pdb .gro files inconsistent with documentation and stdout
- Mark Abraham wrote:
> There are a few python implementations of .trr reading, but I haven't used any of them.
T... - 02:36 PM GROMACS Bug #2824 (Closed): treatment of -ndec for .gro and pdb .gro files inconsistent with documentation and stdout
- the flag -ndec is silently ignored by trjconv in the creation of .gro files. This is in contrast to behavior in at le...
11/23/2018
- 10:58 PM GROMACS Feature #2186: Potential change for logical improvements: move control of constraints purely to the .mdp
- Here's my current thoughts. It makes sense if mdrun makes decisions, AS LONG AS the .log file clearly states, perhaps...
- 01:18 AM GROMACS Bug #2754: Simulated Tempering seems to be broken
- Certainly not a waste of time. The program should be telling you this - I shouldn't have to!
Please, let me know i...
11/22/2018
- 03:05 PM GROMACS Bug #2754: Simulated Tempering seems to be broken
- OK, the basic problem seems to be that if nstexpanded is not set, then it defaults to setting the frequency to @2*ir-...
11/14/2018
- 04:14 AM GROMACS Bug #2754: Simulated Tempering seems to be broken
- Thanks - will take a look when back from a seminar trip Tues/Thurs, will let you know if I cannot reproduce with just...
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