[gmx-users] LJ potential

[Mark Abraham]

----- Original Message -----
From: Sai Pooja <saipooja at gmail.com>
Date: Monday, August 30, 2010 3:33
Subject: Re: [gmx-users] LJ potential
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> 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.

Right, that's totally different from your first question, which implied only protein and thus intra-molecular interactions. When seeking help, you should make sure you  make a complete description the first time, lest you waste everybody's time and effort. That's easier said than done, but you managed to do it on the second attempt :-)

GROMACS allows you to use table lookups for non-bonded interactions, and to use different tables for interactions between different energy groups. So your problem reduces to generating the different tables and groups, and assigning tables to pairs of groups. Aspects of this process are discussed in several places in the manual.

Mark

> 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
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> 
> Institute for Computational Physics
> 
> University Stuttgart
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