[gmx-developers] atomtype-specific forces

Leo leonardo.garma at gmail.com
Mon Dec 13 13:01:25 CET 2010

Hi Berk,

Thanks for the quick reaply.
At the moment I have a test system with 5 atoms, defined with different
atomtypes in the topology (and in the forcefield).
Their values for the typeA variable change as I modify the LJ parameters
(the ones with the same parameters have the same typeA value). So typeA is
not a direct reference to the atomtypes as defined in the topology, which is
what I'm looking for.


2010/12/13 Berk Hess <hess at cbr.su.se>

> Hi,
> 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.
> Berk
> 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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