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From: David Cerutti <dscerutti.gmail.com>

Date: Mon, 9 Sep 2019 13:13:06 -0400

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
*

*>
*

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Received on Mon Sep 09 2019 - 10:30:02 PDT

Date: Mon, 9 Sep 2019 13:13:06 -0400

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:

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Received on Mon Sep 09 2019 - 10:30:02 PDT

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