[gmx-users] constant term in dihedral potential function

[Berk Hess]

> Date: Thu, 28 May 2009 21:49:45 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] constant term in dihedral potential function
> 
> Kukol, Andreas wrote:
> > Hi,
> > 
> > I supply the multiple dihedral terms as a combination of single ones, such as:
> > 
> > ;atom no.              type   phis    k       mult
> > 22    23    24    25     1    180    7.470     1
> > 22    23    24    25     1    0      3.900     2
> > 22    23    24    25     1    180    1.100     3
> > 22    23    24    25     1    90    -5.685     0
> 
> I don't believe this works in the way you might expect. Page 109 of the 
> manual contradicts me, but (undocumented) dihedral type 9 was added 
> recently to allow multiple strictly-consecutive dihedrals of type "1" to 
> be accumulated on the same atoms. Anyway, this can readily be checked by 
> comparing 0-step EM runs, before and after commenting out the last of 
> the multiple dihedrals pre-grompp. Also, you can look at a gmxdump of 
> the .tpr.

This works fine.

> 
> > In case I supply the potential with a Ryckaert-Bellemans dihedral, do I need to exclude the 1-4 interactions between atoms 22 and 25 ?
> 
> The form of the dihedral function doesn't matter. See section 5.4 of the 
> manual.

If you set up the dihedral potential yourself, you choose if to use 1-4 or not.
Your own force-field setup determines if to use 1-4's or not, not the technical way
you supply the potentials in the topology.

> 
> > Maybe one Ryckaert-Bellemans dihedral would be also computationally more efficient ?
> 
> Maybe.

Yes, RB will be computationally more efficient, but the time spent on it is probably negligible.

Berk

> 
> Mark
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