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

[Narjes Khosravian]

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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