[gmx-users] dihedrals potential as a expansion of cosine funtions

Javier Cerezo jcb1 at um.es
Wed Sep 8 19:16:53 CEST 2010

Hi all.

I am a bit confused about how GROMACS handles multiply defined 
interactions in the top file. Concretely, I see from the lipid 
parameters (POPC) from Kukol (JCTC, 5:615, updated in 
http://lists.gromacs.org/pipermail/gmx-users/2010-May/050647.html ) that 
when defining several times an interaction it is sum up. However, it was 
also stated by Mark Abraham that just the last definition in the top 
file is taken into account 

For purposes of GROMACS, a bonded function is defined by the function type
(an integer) and the set of atoms to which it applies. See table 5.4.
There may only be one instance of a given function type for a given set of
atoms. grompp will take the last such function that it finds. Thus you
cannot have multiple periodic dihedral functions on the same four atoms,
even if their multiplicity varies.

Could anyone help me with that? How will GROMACS-4 interpret multiply 
defined interaction?

Many thanks!


Estudiante de Doctorado
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)

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