[gmx-users] Lennard Jones and Buckingham potential together in one simulation

[Mark Abraham]

Hi,

Isn't this covered in those PDFs?

Mark

On Thu, Jun 8, 2017 at 10:34 AM Narjes Khosravian <
narjes.khosravian at chalmers.se> wrote:

> Hi Mark,
>
> Thanks for your reply!
>
> Actually I am using tabulated-potential based on the bellow manual by
> Gareth Tribello.
> <http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf>
>
> <http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf>
> http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf
>
> My problem is that:
>
> Since I have LJ and buckingham both, what should be the statement
> mentioning nbfunc ( and combination-rule) in .top file? e.g. nbfunc=1
> followed by LJ parameters  C and A for the concerned pairs and
>
> then nbfunc=2 (and whatever combination rule) , followed by buckingham
> parameters C, A , B for concerned pairs in the .top file?
>
> I greatly appreciate for any help in this matter.
> Best,
> Narjes
>
>
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark
> Abraham <mark.j.abraham at gmail.com>
> Sent: Thursday, May 4, 2017 3:49:26 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Lennard Jones and Buckingham potential together
> in one simulation
>
> Hi,
>
> This procedure is usually motivated by trying to mix force fields that were
> never intended to be used together, and thus need to be shown work well
> together. In that case, you may as well parameterize a consistent model.
>
> Technically, you might be able to get this to work, but each atom in
> GROMACS can have only one set of VDW parameters, so you need to make the
> same parameters work with both functional forms, and this either impossible
> or tricky. The best bet is using tabulated interactions. Don't try to set
> up your intended target simulation in your first attempt - make something
> simple that lets you prove to yourself you have the interactions working
> the way that you think they should, then add complexity.
>
> Mark
>
> On Wed, May 3, 2017 at 8:41 PM Narjes Khosravian <
> narjes.khosravian at chalmers.se> wrote:
>
> > Dear gromacs users,
> >
> >
> > I am trying to  use Lennard Jones and Buckingham potential  together in
> > one simulation as part of my system is treated by LJ and rest by Buck
> > potential.
> >
> >
> > My question is that how I can include Lennard Jones parameters in
> topology
> > file while my [defaults ] was chosen 2  1 to consider Buckingham
> parameter?
> >
> > I have created table for buck and LJ.
> >
> >
> > I greatly appreciate for any guide in this matter.
> >
> > Narjes
> >
> >
> >  Narjes Khosravian
> >  Postdoc Researcher
> >  Department of Physics, Materials and Surface Theory
> >  Chalmers University of Technology
> >  SE-412 96 Göteborg, Sweden
> >
> > --
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