**From:** *yjcoshc_at_gmail.com*

**Date:** Wed Mar 13 2019 - 10:08:55 CDT

**Next message:**Giacomo Fiorin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**Previous message:**Jérôme Hénin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**In reply to:**Jérôme Hénin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**Next in thread:**Giacomo Fiorin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**Reply:**Giacomo Fiorin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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
*

*>
*

*>
*

**Next message:**Giacomo Fiorin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**Previous message:**Jérôme Hénin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**In reply to:**Jérôme Hénin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**Next in thread:**Giacomo Fiorin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**Reply:**Giacomo Fiorin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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