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

Date: Wed Mar 13 2019 - 10:41:47 CDT

Hi Giacomo,

Thanks for your reply!

Haochuan Chen

在 2019/3/13 下午11:39, Giacomo Fiorin 写道:
> Hi Haochuan, those are special cases (yet rather common, as they are
> default behavior) when the RMSD is computed over the same atoms used
> in the fitting.  The fit gradients happen to be zero, because the
> optimal rotation is by definition the one that minimizes the RMSD, and
> the fit gradients are disabled to save compute time.   For
> eigenvector, it is a more complicated to justify in a sentence, but it
> turns out that the fit gradients also cancel out in the special case
> when the group used in the variable and the group used for fitting
> coincide.
> In your new variable, you should verify first that it behaves like
> RMSD and eigenvector with respect to this, and only in that case
> disable the fit gradients for good. Otherwise, it is probably safer to
> not disable them via a hard-coded instruction but leave the option to
> disable them at run time, which is always available.
> Giacomo
> On Wed, Mar 13, 2019 at 11:10 AM <
> <>> wrote:
> 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, <
>> <>> 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
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD

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