[gmx-users] Defined dihedral function

Dallas Warren dallas.warren at monash.edu
Thu Oct 4 00:03:59 CEST 2018

Chapter 5.8 sets out the way things are defined in the .itp/.top files.

What function the parameters in the ffbonded.itp file follow depends
on the forcefield, so it is specified by the FF itself.

Which function is used by those list of parameters provided in the
ffbonded.itp, you specify in the .itp/.top when you construct the
molecule's topology (Table 5.5) i.e. the ffbonded.itp doesn't specify
the function (not with GROMOS FFs anyway), you do that in your
molecules topology file.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Sat, 29 Sep 2018 at 05:45, Rafa Risnik <rrisnik at gmail.com> wrote:
> Hello all,
> I am trying to add new parameters for a molecule and I have to define
> dihedrals because I'll have different values for the same dihedral
> depending on the position they are in the molecule.
> My question is, where do I define the type o function for the dihedral that
> is defined in the ffbonded.itp? On the ones already there it's only #define
> dih_X_X_X_X and the parameters, there's no identification of the function
> being used.
> Thanks in advance,
> --
> *Rafael R. Romeiro*
> *Ph.D. student - Thermodynamics of biochemical systems*
> *Universidade de São Paulo, Escola Politécnica - Departamento de Engenharia
> Química*
> *GEnBio - Grupo de Engenharia de Bioprocessos (http://sites.usp.br/genbio/
> <http://sites.usp.br/genbio/>)*
> *(11) 96867-2703 / 3091-2282*
> --
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