[gmx-users] constant term in dihedral potential function
gmx3 at hotmail.com
Thu May 28 14:06:35 CEST 2009
> 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
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 ?
Yes, RB will be computationally more efficient, but the time spent on it is probably negligible.
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