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

From: Jérôme Hénin (
Date: Wed Mar 13 2019 - 09:37:31 CDT

Dear Haochuan,

Yes. That is handled at the atom group level by enableFitGradients, which
defaults to true. Cases where the calculation is not supported will trigger
a dependency failure, so you cannot miss them.


On Wed, 13 Mar 2019 at 14:04, <> wrote:

> 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?
> Thanks,
> Haochuan Chen

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