[gmx-developers] atomtype-specific forces

Berk Hess hess at cbr.su.se
Mon Dec 13 12:32:31 CET 2010


t_mdatoms contains an array typeA which contains the atom types.

But any type of (pairwise) non-bonded interaction that depends linearly
on the charges
and/or LJ parameters can be passed through the user tables. This can be made
atomtype specific using the energgrp and energygrp_table mdp options.
So I think you wouldn't need to do any coding at all.


On 12/13/2010 12:28 PM, Leo wrote:
> Hello,
> I am trying to implement a new non-bonded interaction in GROMACS that
> should only be applied to certain atom types.
> I already figured out how to modify the existing interactions and how
> to implement new forces, but I still don't know how to apply them only
> to a specific atom type. The t_mdatoms struct doesn't seem to include
> any atomnames or atomtypes variables, so I was wondering if I should
> include one (just copying it from t_atoms, in the same way as all the
> other variables are copied in the atoms2md() function) and use it to
> restrict the application of the new forces based on the atomtypes/names.
> It looks a bit complicated to handle the problem this way, so could
> you think of a better solution (e.g. using the parameters already
> available in the t_mdatoms struct)?
> Leonardo Garma
> Graduate Student
> University of Oulu
> Biochemistry Department

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