[gmx-users] LJ potential

[Mark Abraham]

----- Original Message -----
From: Sai Pooja <saipooja at gmail.com>
Date: Tuesday, August 31, 2010 2:45
Subject: Re: [gmx-users] LJ potential
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> 
> Thanks Mark. I have just 2 more queries regarding this. >   > When using tables for the potential,  >   > 1) For VdW interactions, it it alright to use the topology file generated by pdb2gmx using a forcefield (eg. CHARMM27) which specifies LJ paramters as 'sigma' and 'epsilon' instead of C6 and C12 as in the case of user defined potentials?   >   > I ask this because I get a warning when I try to do the above: > :WARNING 2 [file initffd.top, line 8082]:
>   Using sigma/epsilon based combination rules with user supplied potential
>   function may produce unwanted results

You will need to take suitable care. grompp will only use the combination rules if it cannot find an existing definition for that pair of atomtypes, so if you make all the definitions, you should be OK. A good way to test that you are on the right track is whether you can produce an energy group + table file that will reproduce the result GROMACS gets if you leave it alone.
  
 > 2) If one is interested in using PME for electrostatic interactions but with different electrostatic interaction functions for different pairs of energygrps, is it alright to specify the simple coulomb function in the user defined table and use the PME-User option for coulombtype?

Probably not. The form of the reciprocal-space PME term presupposes a simple Coulomb function on all atoms. So did the parameterization of the force field, so you're already taking your life in your hands :-)

Mark

  > On Sun, Aug 29, 2010 at 7:54 PM, Mark Abraham <mark.abraham at anu.edu.au> wrote:
  > 
> 
> ----- 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
  > > 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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