[gmx-users] LJ potential

[Sai Pooja]

Hi,

I am simulating a system of a protein in water. I am trying to run the
simulation with a modified protein-water LJ and coulomb interaction. Since
LJ and  coulomb interaction parameters are defined at the atomic level in
the forcefield files, I cannot figure out a good way to modify them for
protein-water interactions specifically. In other words, I want to modify
the protein water interaction without altering protein-protein interaction.

Pooja


On Tue, Aug 24, 2010 at 8:31 AM, Florian Dommert <
dommert at icp.uni-stuttgart.de> wrote:

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> On 08/24/2010 02:27 PM, Sai Pooja wrote:
> > Hi,
> >
> > If there are n types of atoms in protein, how does one specify:
> > 1) Different types of LJ non-bonded interactions for different pairs?
> > 2) Modified Coloumb(by a pre-multiplier) interactions for different
> pairs?
> >
> > Pooja
> >
> >
>
> Hi,
>
>  this can be defined in the top file. Take a look at the manual
> regarding the force field and different function types for the nonbonded
> interactions. This will surely help.
>
> /Flo
>
> - --
> Florian Dommert
> Dipl.-Phys.
>
> Institute for Computational Physics
>
> University Stuttgart
>
> Pfaffenwaldring 27
> 70569 Stuttgart
>
> Phone: +49(0)711/685-6-3613
> Fax:   +49-(0)711/685-6-3658
>
> EMail: dommert at icp.uni-stuttgart.de
> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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