[gmx-users] constant term in dihedral potential function
Mark Abraham
Mark.Abraham at anu.edu.au
Tue May 26 17:40:48 CEST 2009
Kukol, Andreas wrote:
> 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.
This is only relevant if you're ever using the magnitude of the
potential energy for something. d/dr of such a term is zero, of course,
so there's no force contribution and thus it does not affect the
dynamics at all.
Mark
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