[gmx-users] gromos force field

[Patrick Fuchs]

Hi,
I'm coming late, but I may add a few words. The GROMOS force fields have 
been parameterized with the GROMOS software using a twin-range cutoff 
(0.8/1.4), but this option is no longer available in recent versions of 
GROMACS. However, in a recent study 
(https://doi.org/10.1021/acs.jctc.8b00758), it was showed that using a 
single range cutoff (rlist = rcoulomb = rvdw = 1.4 and nstlist = 1) + 
reaction field (coulombtype = Generalized-Reaction-Field) together with 
the group scheme for neighbor searching (cutoff-scheme=group, even if 
this is deprecated since version 5.1, it is still usable) reproduces 
results generated with the GROMOS software and FF. One other study on 
lipids points to the same conclusion regarding the use of single range 
cutoff (https://doi.org/10.1021/acs.jctc.7b00178) as an alternative to 
twin-range cutoff. That was also tested in this redmine issue: 
https://redmine.gromacs.org/issues/1400. This solution increases 
significantly the computational cost compared to former twin-range 
cutoff, but it is probably the one which gives the closest results to 
the original GROMOS FF.
Alternatively, it was found in a recent paper 
(https://pubs.acs.org/doi/10.1021/acs.jctc.8b00425) that it is possible 
to use the Verlet scheme for neighbour searching with rvdw = 1.2 and PME 
for electrostatics (with rcoulomb = 1.2 since it has to equal rvdw) as 
an acceptable option to reproduce some liquid properties calculated with 
the GROMOS software.
Regarding the remark about the GROMOS software, I'm not aware of any 
"problems".
Best,

Patrick

Le 23/09/2019 à 12:49, Justin Lemkul a écrit :
>
>
> 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
>