[gmx-users] constant term in dihedral potential function

[Kukol, Andreas]

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

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

Many thanks
Andreas

-----------------------
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Berk Hess
Sent: 26 May 2009 09:46
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] constant term in dihedral potential function

Hi,

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.

Berk

> 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
> Andreas
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