Re: [gmx-users] Reaction Field approach with GROMACS

[Mark Abraham]

Hi,

To clarify, that issue was unrelated to RF. Multiple time stepping in the
group scheme needed fixing, and was fixed. However, it was removed before
version 2016, as a precursor to removing the group scheme. Moreover, even
before that, you can't compare results with GROMOS MTS if its
implementation is still the same irreversible one that we corrected before
GROMACS 4.5 to a Trotter style one (modulo bug 1400).

Mark

On Thu, 1 Sep 2016 20:58 Justin Lemkul  wrote:

>
>
> On 9/1/16 2:38 PM, ABEL Stephane 175950 wrote:
> > Hi All,
> >
> > I have a question about the reaction field approach used by GROMACS. I
> have seen that in earlier version (V.4.6.X andn 4.5.3) there was a bug with
> the Reaction Field approach (http://redmine.gromacs.org/issues/1400). It
> is corrected in the GROMACS version than 5.0 or in lastest version one
> (e.g. 2016)? Can I use safely this approach to compare my results with
> those obtained with the GROMOS program?
> >
>
> It was fixed in 5.0, so that version and anything newer is fine.
>
> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Reaction Field approach with GROMACS

[Justin Lemkul]

On 9/1/16 2:38 PM, ABEL Stephane 175950 wrote:

Hi All,

I have a question about the reaction field approach used by GROMACS. I have 
seen that in earlier version (V.4.6.X andn 4.5.3) there was a bug with the 
Reaction Field approach (http://redmine.gromacs.org/issues/1400). It is 
corrected in the GROMACS version than 5.0 or in lastest version one (e.g. 
2016)? Can I use safely this approach to compare my results with those obtained 
with the GROMOS program?



It was fixed in 5.0, so that version and anything newer is fine.

http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Reaction Field approach with GROMACS

[ABEL Stephane 175950]

Hi All, 

I have a question about the reaction field approach used by GROMACS. I have 
seen that in earlier version (V.4.6.X andn 4.5.3) there was a bug with the 
Reaction Field approach (http://redmine.gromacs.org/issues/1400). It is 
corrected in the GROMACS version than 5.0 or in lastest version one (e.g. 
2016)? Can I use safely this approach to compare my results with those obtained 
with the GROMOS program?

Thanks

Stéphane
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