[gmx-developers] atomtype-specific forces

[Berk Hess]

grompp renumbers atom types with the same LJ parameters.
Then you should use grompp -norenum

Berk

On 12/13/2010 01:01 PM, Leo wrote:
> 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.
>
> Leo.
>
> 2010/12/13 Berk Hess <hess at cbr.su.se <mailto: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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