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

From: yjcoshc_at_gmail.com
Date: Wed Mar 13 2019 - 10:08:55 CDT

Dear Jérôme,

I changed my code to use enable(f_ag_fit_gradients) and it seems I get
the correct gradients! Thanks a lot!

By the way, I have seen that the constructor of colvar::rmsd and
colvar::eigenvector uses disable(f_ag_fit_gradients), and that's why I
also disable it in my class constructor. Why is the feature disabled in
these cases?

Best regards,

Haochuan Chen

在 2019/3/13 下午10:37, Jérôme Hénin 写道:
> 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.
>
> Best,
> Jérôme
>
> On Wed, 13 Mar 2019 at 14:04, <yjcoshc_at_gmail.com
> <mailto:yjcoshc_at_gmail.com>> 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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