[gmx-users] GROMOS forcefields

[shakira shukoor]

Thank you for such a detailed response. The explanation was very helpful.

On Sat, Jan 4, 2020 at 10:00 PM Kenny Goossens <goossens_kenny at hotmail.com>
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.
>
> With kind regards,
> ______________________________
> Kenneth Goossens, PhD student
> Laboratory of Medicinal Chemistry (Building A - Room 2.13)
> University of Antwerp - Campus Drie Eiken
> Universiteitsplein 1
> B-2610 Wilrijk
> Belgium
>
>
> ________________________________
> Van: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> namens shakira shukoor
> <shakirashukoor1993 at gmail.com>
> Verzonden: zaterdag 4 januari 2020 16:23
> Aan: gromacs.org_gmx-users at maillist.sys.kth.se <
> gromacs.org_gmx-users at maillist.sys.kth.se>
> Onderwerp: [gmx-users] GROMOS forcefields
>
> Hi all
> Can anyone explain the different code seen in forcefields of GROMOS like
> 53A6, 54A7, 43a1,..... what does these numbers mean?
>
> --
> *Best Regards*
>
> Shakkira E
> PhD student INSPIRE Scholar
> Department of Chemistry
> sdmdlab.xyz
> IIT Patna
> Bihta
> Patna 801106
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-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106