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Justin Lemkul

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12/11/2018

07:30 PM GROMACS Revision 29b7c742: Fixed Thole generation.

11/08/2018

04:10 AM GROMACS Feature #2451: Linear virtual sites with fixed distance
Even worse, with version 2018, the virtual site construction throws an error that cannot be circumvented. I haven't t...

11/06/2018

06:34 PM GROMACS Feature #2451: Linear virtual sites with fixed distance
To follow up on this issue, I have tried to do what Berk suggested with 3fd construction, and it indeed works just fi...

10/19/2018

12:49 AM GROMACS Feature #1168 (In Progress): g_density does not do what users think it does, given PBC over z and constant pressure simulation
Updating status to reflect Chris' latest comment about the issue still persisting.

10/04/2018

04:05 PM GROMACS Revision c7830c47: Made conversion of Drude bonds to hyperpolarization cleaner.
04:04 PM GROMACS Revision ad1cbe41: Fixed LP pair/exclusion generation and updated LP
construction constants for disulfides.

08/23/2018

02:08 PM GROMACS Feature #2622: Reduce severity of Berendsen warning
Mark Abraham wrote:
> Justin Lemkul wrote:
> > I have noticed in the latest version that any use of Berendsen coupl...

08/22/2018

03:43 PM GROMACS Feature #2622: Reduce severity of Berendsen warning
Berk Hess wrote:
> I disagree on 1), since a Bussi thermostat has all the advantages of the Berendsen thermostat, bu...
01:37 PM GROMACS Feature #2622 (New): Reduce severity of Berendsen warning
I have noticed in the latest version that any use of Berendsen coupling algorithms prompts a warning, causing grompp ...

03/17/2018

04:35 PM GROMACS Feature #2451: Linear virtual sites with fixed distance
David van der Spoel wrote:
> Just wondering whether fixing the 3FAD such that it can deal with 180 degree angles wou...

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