It seems like, it does not transmute back to Cartesian coordinates, but
uses the finite difference method to calculate the force (respect to phi
and psi)
On Fri, Sep 6, 2019 at 1:29 AM David Cerutti <dscerutti.gmail.com> wrote:
> You've got two dihedral angles, A-B-C-D and B-C-D-E. The potential energy
> is computed using bicubic spline interpolation on a grid of values,
> typically 24 x 24 point in each direction (the potential is known at 15
> degree intervals, and interpolated based on that). The forces on atoms are
> computed form the derivatives of that bicubic spline interpolation, which
> must then be transmuted via the chain rule back to Cartesian space on each
> of the atoms.
>
> HTH,
>
> Dave
>
>
> On Thu, Sep 5, 2019 at 6:35 PM Lod King <lodking407.gmail.com> wrote:
>
> > Hi Amber
> >
> > How to explicitly understand the force computed from U(CMAP) energy
> term. I
> > have been reading the papers "Mackerell, Feig, and Brooks Vol. 25, No. 11
> > Journal of Computational Chemistry" and "Martin Karplus 1995 Journal of
> > Computational Chemistry", and still having difficulty understanding the
> > math applied here.
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> >
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Received on Fri Sep 06 2019 - 17:30:03 PDT
