GROMACS development

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...