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

[Mark Abraham]

Hi,

That pdf twice specifies the correct value for nbfunc. For example, the
last sentence of section 1. I don't understand where the confusion lies.

Mark

On Thu, 8 Jun 2017 10:46 Narjes Khosravian <narjes.khosravian at chalmers.se>
wrote:

> Is there any guideline for that?
>
>
> My exact question is about topology file for  using tabulated potential.  What
> should be the statement
> mentioning nbfunc ( and combination-rule) in .top file when I wanted to
> have both potential (LJ and BKS)?
>
> Best,
> Narjes
>
>
>  Narjes Khosravian
>  Postdoc Researcher
>  Department of Physics, Materials and Surface Theory
>  Chalmers University of Technology
>  SE-412 96 Göteborg, Sweden
>
>
> *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, June 8, 2017 10:38:01 AM
>
> *To:* gmx-users at gromacs.org
> *Subject:* Re: [gmx-users] Lennard Jones and Buckingham potential
> together in one simulation
> 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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