You can check the various codes--perhaps the easiest to access is mdgx,
based on the DLPoly implementation. Look in the file BondContrib.c, which
is #include'd multiple times in Bonded.c. On line 471 of BondContrib.c,
there is the comment "// Transform the dihedral forces to cartesian
coordinates." It's all a bunch of chain rules--the transformation for
angular forces is a bit easier to hash through, but in each case you can
verify that the fomulaic sums of forces on all atoms add to zero. The
conversion of two-body forces to Cartesian space also rests on a chain
rule, but it's so simple and intuitive that the technicality is often
overlooked.
Cheers,
Dave
On Mon, Jan 22, 2018 at 3:00 PM, Siddhartha Jain <tmfs10.gmail.com> wrote:
> Hi,
>
> So from what I've been reading, AMBER force field has terms that depend on
> the dihedral angle. However if you ask for gradients via sander, you get
> gradients for the cartesian space. So I'm guessing that in the function to
> compute the energy, there's a transformation from cartesian to torsion
> space?
>
> What transformation is used?
>
> Thanks
> --Sid
>
> --
> https://tmfs10.github.io
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Received on Mon Jan 22 2018 - 14:00:02 PST
