[gmx-users] constant term in dihedral potential function
gmx3 at hotmail.com
Tue May 26 10:46:13 CEST 2009
I don't know how you currently supply your dihedral (multiple periodic dihedral terms?).
But you can supply the whole potential, including the constant term, using a Ryckaert-Bellemans dihedral.
The manual gives some conversion formulas.
> From: a.kukol at herts.ac.uk
> To: gmx-users at gromacs.org
> Date: Tue, 26 May 2009 09:29:36 +0100
> Subject: [gmx-users] constant term in dihedral potential function
> Dear all,
> I included the following dihedral potential function in a topology:
> V(phi2) = -5.865 + 7.470 [1+cos(phi2-180°)] + 3.99 [1+cos(2 phi2)] + 1.1 [1+cos(3 phi2-180°)]
> The problem is about representing the constant term -5.865. Using equation 4.61 (Gromacs 4.0 manual):
> V(phi) = k * (1 + cos (n phi - phis) )
> I specified:
> V = -5.865 * (1 + cos (0 - 90) ) = -5.865 with multiplicity n=0
> That leads to the entry in the topology file:
> 22 23 24 25 1 90 -5.685 0
> This worked fine in Gromacs 3.3, but in Gromacs 4.05 I get the error message (from Grompp):
> Fatal error:
> Value of 'multiplicity' in Proper Dih. is 0, which is smaller than the minimum of 1
> I wonder, if this is a bug in Gromacs 4.05, or if there is any better way to specify a constant term in a dihedral potential function.
> Many thanks
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