[gmx-users] gromos force field

Justin Lemkul jalemkul at vt.edu
Mon Sep 23 12:49:52 CEST 2019

On 9/21/19 12:44 PM, p buscemi wrote:
> Dear Users,
> I often use Gromos force field because ATB provides top files for reasonably large molecules - 1000 atoms. With Gromacs 2019.3 the error now appears:
> The GROMOS force fields have been parametrized with a physically
> incorrect multiple-time-stepping scheme for a twin-range cut-off. When
> used with a single-range cut-off (or a correct Trotter
> multiple-time-stepping scheme), physical properties, such as the density,
> might differ from the intended values. Check if molecules in your system
> are affected by such issues before proceeding. Further information may be
> available at https://redmine.gromacs.org/issues/2884.
> while message is clear enough, just how large an error in density is anticipated ? A 10 % error in polymer solution may be tolerable. A 2 % error in a crystal or binding site may be a concern.
> Gromacs indicated that Gromos may be dropped for v 2020. Is there no other option - llike fixing the time-stepping-scheme. Or must I not use the twin-cutoff typically presented in the mpd files ?
> There is a conversion from Gromos top to Amber, but would not the error be translated as well ?

The problem is that the GROMOS force fields were derived using software 
that has problems, therefore rendering all of the behaviors of this 
force field in other software questionable. There should be a paper 
forthcoming from the core developers that describes the situation 
sometime soon.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129


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