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From: Lod King <lodking407.gmail.com>

Date: Mon, 9 Sep 2019 10:53:56 -0700

Thanks for the guidance and path. Indeed, there is no finite difference

calculation in the code

So, it seems to me that code is to compute the E(CMAP) while the phi/psi

angles are changed to coordinates during the conversion steps, and then, by

taking the derivate of the E(MAP) which already with respect to coordinates

to compute the force.

On Mon, Sep 9, 2019 at 10:13 AM David Cerutti <dscerutti.gmail.com> wrote:

*> You can look in the pmemd code for the derivative calculations--the file is
*

*> going to be ${AMBERHOME}/src/pmemd/src/cuda/kBWU_cmap.h. You can thank /
*

*> blame me for making all of the little includables. There is no finite
*

*> difference calculation, it's a straight-up change-of-coordinates chain rule
*

*> application. You can also look in mdgx,
*

*> ${AMBERHOME}/AmberTools/src/mdgx/BondContrib.c, to see a different
*

*> expression of the same thing for dihedrals. The CMAP is two dihedral
*

*> angles, computed one after the other. I think the only difference is that
*

*> the magnitude of the force comes not from computing [ K cos(N theta) ] but
*

*> rather evaluating the bicubic spline for magnitude and derivative in each
*

*> dimension. The chain rule for each set of four atoms A-B-C-D and B-C-D-E
*

*> should be the same as for the standard dihedrals after that. I'm working
*

*> in that code myself to try and port CMAP functionality to mdgx.
*

*>
*

*> Dave
*

*>
*

*>
*

*> On Fri, Sep 6, 2019 at 8:21 PM Lod King <lodking407.gmail.com> wrote:
*

*>
*

*> > 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.
*

*> > > > _______________________________________________
*

*> > > > AMBER mailing list
*

*> > > > AMBER.ambermd.org
*

*> > > > http://lists.ambermd.org/mailman/listinfo/amber
*

*> > > >
*

*> > > _______________________________________________
*

*> > > AMBER mailing list
*

*> > > AMBER.ambermd.org
*

*> > > http://lists.ambermd.org/mailman/listinfo/amber
*

*> > >
*

*> > _______________________________________________
*

*> > AMBER mailing list
*

*> > AMBER.ambermd.org
*

*> > http://lists.ambermd.org/mailman/listinfo/amber
*

*> >
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
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*> http://lists.ambermd.org/mailman/listinfo/amber
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*>
*

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Received on Mon Sep 09 2019 - 11:00:02 PDT

Date: Mon, 9 Sep 2019 10:53:56 -0700

Thanks for the guidance and path. Indeed, there is no finite difference

calculation in the code

So, it seems to me that code is to compute the E(CMAP) while the phi/psi

angles are changed to coordinates during the conversion steps, and then, by

taking the derivate of the E(MAP) which already with respect to coordinates

to compute the force.

On Mon, Sep 9, 2019 at 10:13 AM David Cerutti <dscerutti.gmail.com> wrote:

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Received on Mon Sep 09 2019 - 11:00:02 PDT

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