Michael Shirts
- Registered on:
- Last connection: 03/01/2020
Issues
- Assigned issues: 20
- 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
03/01/2020
- 03:23 PM GROMACS Bug #3304: Failure in Log Output for Expanded Ensemble Weights using Simulated Tempering in GROMACS 2019.5
- Will put it on my todo list.
- 03:22 PM GROMACS Feature #3363: Improve FEP testing
- I don't have the time to pull everything out now that failed in the past, but by feeling has been that the majority o...
02/26/2020
- 05:53 PM GROMACS Feature #3363: Improve FEP testing
- Current plan:
- Put in folder FreeEnergy/
- each test has own folder.
- put .top/.gro/.itp/README.txt in each su...
01/30/2020
- 05:06 AM GROMACS Feature #3363: Improve FEP testing
- Systems:
We want to test:
* intra and intermolecular interactions. Suggest a ethanol-like molecule, with LJ o...
01/03/2020
- 09:36 PM GROMACS Feature #2070: Physical validation testing
- Pascal, can you be a bit more specific than: "is available"? Maybe review briefly what is incorporated now (which te...
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...
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