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Michael Shirts

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  • Last connection: 08/10/2019

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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 (Fix uploaded): 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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