[gmx-users] About "Apply Multiple bonded interactions" for dihedral potential definition

Justin A. Lemkul jalemkul at vt.edu
Sat Jan 23 15:17:37 CET 2010

WU Yanbin wrote:
> Hi, all,
> According to Manual v3.3, "It's possible to apply multiple bonded 
> interactions of the same type on the same atoms" [12th line of Page 98].
> If a dihedral potential for 4 neighboring atoms is defined 3 times using 
> the "periodic type" in the topology file, like
> V=k1*(1+cos(phi-phi_s1))
> V=k2*(1+cos(2*phi-phi_s2))
> V=k3*(1+cos(3*phi-phi_s3))
> would GROMACS recognize the dihedral potential as the sum of the above 
> three, or just the 3rd one (which is defined last)?
> If GROMACS recognizes the dihedral potential as the sum, then this can 
> be another way to define OPLS force filed in GROMACS.

Bonded interactions are summed.  Surely this is in the manual somewhere, but it 
certainly has been discussed in the list archive many times.

I think you might find this discussion relevant:



> Does anyone know the answer? Thanks.
> Best,
> Yanbin


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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