Thank you for such a detailed response. The explanation was very helpful. On Sat, Jan 4, 2020 at 10:00 PM Kenny Goossens <goossens_ke...@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-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> namens shakira shukoor > <shakirashukoor1...@gmail.com> > Verzonden: zaterdag 4 januari 2020 16:23 > Aan: gromacs.org_gmx-users@maillist.sys.kth.se < > gromacs.org_gmx-users@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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
