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

Mark Abraham mark.abraham at anu.edu.au
Wed Sep 8 22:25:36 CEST 2010

----- Original Message -----
From: Javier Cerezo <jcb1 at um.es>
Date: Thursday, September 9, 2010 3:17
Subject: [gmx-users] dihedrals potential as a expansion of cosine funtions
To: gmx-users at gromacs.org

> 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 (http://lists.gromacs.org/pipermail/gmx-users/2007-
> January/025316.html):Quote:
> <<
> 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?

GROMACS behaves differently when looking up parameters for a dihedral function from the [dihedraltypes] than when assembling dihedral functions whose parameters are already supplied in [dihedrals]. (Some time since 2007 you will find a post from Berk that corrects me on this point :-)) The GROMOS forcefields use the latter method via the gb_xx cpp macros. These add. You can verify this simply by adding a duplicate of a single [dihedral] and observing that the Step 0 energy will change.

Normal [dihedraltypes] of the same "kind" do not add, except for type 9 (introduced in GROMACS 4.5) which caters to aspects of CHARMM and AMBER force fields.

Now that I think about it, perhaps a sentence is needed in the manual treating this case. Will check there.


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