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.
Mark
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