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Michael Shirts

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  • Last connection: 03/05/2019

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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...

09/23/2018

06:34 AM GROMACS Task #1868: implement mdrun -rerun better, simplifying do_md
> Maybe just don't report the virial unless explicitly requested (with an error if not possible). Preserving old beha...

08/30/2018

04:04 AM GROMACS Task #2616: Model for MD state
> Where do we already already need copies of state objects (such as t_state in minimize)? And are there exceptions ei...

12/30/2017

10:29 PM GROMACS Bug #2264: Changes in bonded interactions are not considered in expanded ensemble simulations
So, I believe there may be an error here (there are lots of different ways of doing the settings that have not all be...

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