**From:** *yjcoshc_at_gmail.com*

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

**Next message:**Jérôme Hénin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**Previous message:**Norman Geist: "BUG? reinitatoms on wrapped coordinates occasionally fail with rigidbonds"**Next in thread:**Jérôme Hénin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**Reply:**Jérôme Hénin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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:**Jérôme Hénin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**Previous message:**Norman Geist: "BUG? reinitatoms on wrapped coordinates occasionally fail with rigidbonds"**Next in thread:**Jérôme Hénin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**Reply:**Jérôme Hénin: "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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