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Tyler Reddy

  • Registered on: 07/22/2016
  • Last connection: 12/27/2016

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12/27/2016

10:53 PM GROMACS Bug #2094 (New): Solvation Consistency with MARTINI forcefield water across GROMACS versions with user-specified VDW size
Although it is known that GROMACS database VDW size parameters for solvation changed with the 5.0 series, it is not c...

10/31/2016

12:20 PM GROMACS Bug #2014: GROMACS free energy memory footprint
I don't think reducing the timestep or conventional techniques for equilibration work if the starting coordinates are...

10/19/2016

03:50 PM GROMACS Bug #2014: GROMACS free energy memory footprint
My use case is pretty strange, but very useful to me. I think the entire run is basically FE, right? All steps are cl...

08/09/2016

05:12 PM GROMACS Bug #2014: GROMACS free energy memory footprint
I don't see any commits in release-2016 since August 4/ 2016. Does it take a while for them to show up on redmine / g...

07/30/2016

06:12 PM GROMACS Bug #2014: GROMACS free energy memory footprint
I've produced and confirmed a 'minimum failing example' which also has some additional debug information and observat...

07/28/2016

08:13 PM GROMACS Bug #2014: GROMACS free energy memory footprint
I'm running on a single core for various reasons: 1) the purpose of the lambda-growth process is to resolve steric co...
05:47 PM GROMACS Bug #2014: GROMACS free energy memory footprint
I've attached a log file for the 3 million particle slow-growth memory failure case. The memory failure appears to oc...

07/22/2016

05:30 PM GROMACS Bug #2014 (Closed): GROMACS free energy memory footprint
Erik asked me to open an issue related to my observations below (pasted from my original email). I'll endeavour to pr...

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