[gmx-users] constant term in dihedral potential function

[Kukol, Andreas]

Many thanks for your help.

As for the 1-4 interactions, I am using the Gromos53a6 forcefield for everything apart from this particular dihedral.

I did not exclude 1-4 interactions previously with the multiple dihedral terms. Does this mean, if I use Ryckaert-Bellemans now (yielding the same potential function), I don't need to make any changes to 1-4 interactions ?

Note that the previous method has been validated (with Gromacs 3.3), the problem is that it doesn't work with Gromacs 4 anymore. So I am trying to achieve the same result with Ryckaert-Bellemans instead of multiple periodic dihedrals.

Many thanks
Andreas

-----------------------
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Berk Hess
Sent: 28 May 2009 13:07
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] constant term in dihedral potential function



> 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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