[gmx-users] GROMOS forcefields

[Justin Lemkul]

On 1/4/20 11:29 AM, Kenny Goossens wrote:
> Hi Shakkira,
>
> In each of the consecutice iterations of the GROMOS force field, a reparameterization of the constants was performed in order to reproduce experimental data for various molecules (in the case of the GROMOS suite, parameterization is mainly fitted to free enthalpy of solvation). For GROMOS54a7, the focus was on improving behaviour of amino acids. Older iterations of the force field have less parameters, and are in general less accurate. This depends on the system you are working with, however. The first number (43,56,...) stands for the number of atom types in the force field, the last number stands for the iteration of the force field. Also not that A and B versions are designed for different types of applications.
>
> I would advise you to look into the literature on the parameterization of the force fields to get an idea of the improvements/changes in every iteration of the force field. Furthermore, beware as the GROMOS force field does not always show the intended behavior in newer versions of Gromacs, and extra caution has to be taken in deciding on the simulation conditions. The issues are illustrated i.e. in Reißer 2017m JCTC (10.1021/acs.jctc.7b00178) And Silva et al 2018 JCTC (10.1021/acs.jctc.8b00758). As far as I'm aware, the Gromacs team has decided to discontinue support for GROMOS in the future for this reason.

Another 2018 paper accused GROMACS of being buggy: 
https://pubs.acs.org/doi/10.1021/acs.jctc.8b00425 - that study has 
motivated the response from the core GROMACS developers 
(https://chemrxiv.org/articles/On_The_Importance_of_Accurate_Algorithms_for_Reliable_Molecular_Dynamics_Simulations/11474583/1) 
illustrating defects in the physical model used to derive many of the 
the GROMOS parameter sets; it's not a bug in GROMACS that is likely the 
issue.

-Justin

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Justin A. Lemkul, Ph.D.
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