Thanks a lot, Dr. Cerutti,
"which must then be transmuted via the chain rule back to Cartesian space
on each of the atoms", this is exactly what I need to fully understand. I
read Karplus' paper explained about the dihedral term for the force.
Any suggestions if I should read "vector papers/textbooks or consult a math
professor?
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 - 02:30:02 PDT
