Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?

Date: Wed Mar 13 2019 - 08:01:04 CDT

Dear NAMD and Colvars developers,

If I have a vector *v* = *R* * *X* - *X*_ref, where the *X* is current
Cartesian coordinates of a set of atoms, *X*_ref is the reference
coordinates and *R* is the optimal rotation matrix, and in the C++
interface I have correctly setup the ref_pos of atom_group *X* in the
C++ interface. Assuming I have a scalar function f(*v*) and I know the
derivative of f with respect of *v* (df/d*v*), can I use df/d*v *as the
atomic gradients of atom_group *X*? In other words, can I assume
d*R*/d*X* is automatically computed when I have setup b_rotate and
ref_pos of *X* in the atom_group initialization?


Haochuan Chen


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