[gmx-users] change coloumb interaction
sanni at theochem.uni-frankfurt.de
Tue Jun 24 17:27:34 CEST 2008
Thank you Mark for your fast and helpful suggestion !
I read the manual concerning the user defined potential (manual 6.6 and
7.3.11) and I have again some question :
1. In the mdp file I chose : energygrps: Protein SOL
energygrp_table : Protein SOL
So would that mean that GROMACS treat o n l y the interaction between the
atoms in the group Protein and the atoms in the group SOL according to a
"table_Protein_SOL.xvg" file ?
Or do I have to specify the groups in another way ?
2. I created the "table_Protein_SOL.xvg" file but GROMACS asks also for a file
"table_Protein_SOL_Protein_SOL.xvg". What should be the content of this
Thank you in advance
> 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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