[gmx-users] change coloumb interaction

Mark Abraham Mark.Abraham at anu.edu.au
Sat Jun 21 22:00:42 CEST 2008

Sang-Min Park wrote:
> Dear all,
> I want to change (for example : 2 times the 'normal' value) only the 
> coloumb interaction between the solvent and a small peptide molecule. On 
> the other hand the interaction  SOL-SOL and peptide-peptide should be 
> according to the standard given parameters of GROMACS.
> The change of the charges would be not the solution, because this would 
> cause also a change in the SOL-SOL and pep-pep coloumb interaction.
> For example for the LJ Potential the change of the interaction potential 
> (only the interaction) can be done easily when one scale the nonbonded 
> interaction parameters. Furthermore one has to define some new atomtypes..
> For the coulomb interaction I think I have to modify the source code 
> concerning the ewald summation, e.g. I have to multiply all 
> contributions SOL-PEP with a scaling factor a.
> So related to the mentioned problem I have the following question:
> In which file and where there I have to make the changes ?

If you use the tabulated non-bonded functions in GROMACS (manual section 
6.6) and the facility to specify different such tables for different 
pairs of groups (7.3.11), then you can probably achieve this effect 
without touching the code. Simplest would be to do a quick "normal" 
calculation that somehow dumps the usual table.xvg and then to modify it 
as you desire, but I am not sure how to get such a dump. Perhaps others 
can suggest a good way.


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