AMBER Archive (2009)

Subject: Re: [AMBER] dihedral force calculation

From: case (case_at_biomaps.rutgers.edu)
Date: Sat Sep 12 2009 - 09:04:34 CDT

On Fri, Sep 11, 2009, Germain Vallverdu wrote:
>
> I am trying to understand the cartesian forces calculations in the case
> of a dihedral potential. The source code of this calculation is in
> dihedrals.f90 module.
>
> I supposed that the following is used
>
> f = - d E(phi) / d r = 1/sin phi * dE(phi)/d phi * d cos phi / d r

This fails when sin phi is close to zero. Generally speaking, you want to
carry out the calculation as follows:

f = - d E(phi) / d r = - (dE(phi)/d cos phi) * (d cos phi / d r)

> I juste would like to know if my previous equation is right. Mainly is
> the minus sign correct ?

Not sure which "minus sign" you mean. Amber programs collect the "force"
which is the negative of the gradient with respect to cartesian coordinates.

...hope this helps...dac

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