**From:** *yjcoshc_at_gmail.com*

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

**Next message:**Brian Radak: "Re: Re: Didn't Find vdw parameter QMMM"**Previous message:**Giacomo Fiorin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**In reply to:**Giacomo Fiorin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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
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*> default behavior) when the RMSD is computed over the same atoms used
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*> in the fitting. The fit gradients happen to be zero, because the
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*> optimal rotation is by definition the one that minimizes the RMSD, and
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*> the fit gradients are disabled to save compute time. For
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*> eigenvector, it is a more complicated to justify in a sentence, but it
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*> turns out that the fit gradients also cancel out in the special case
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*> when the group used in the variable and the group used for fitting
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*> coincide.
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*>
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*> In your new variable, you should verify first that it behaves like
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*> RMSD and eigenvector with respect to this, and only in that case
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*> disable the fit gradients for good. Otherwise, it is probably safer to
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*> not disable them via a hard-coded instruction but leave the option to
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*> disable them at run time, which is always available.
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*>
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*> Giacomo
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*>
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*>
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*> On Wed, Mar 13, 2019 at 11:10 AM <yjcoshc_at_gmail.com
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*> <mailto:yjcoshc_at_gmail.com>> wrote:
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*>
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*> Dear Jérôme,
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*>
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*> I changed my code to use enable(f_ag_fit_gradients) and it seems I
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*> get the correct gradients! Thanks a lot!
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*>
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*> By the way, I have seen that the constructor of colvar::rmsd and
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*> colvar::eigenvector uses disable(f_ag_fit_gradients), and that's
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*> why I also disable it in my class constructor. Why is the feature
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*> disabled in these cases?
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*>
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*> Best regards,
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*>
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*> Haochuan Chen
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*>
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*>
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*> 在 2019/3/13 下午10:37, Jérôme Hénin 写道:
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*>> Dear Haochuan,
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*>>
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*>> Yes. That is handled at the atom group level by
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*>> enableFitGradients, which defaults to true. Cases where the
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*>> calculation is not supported will trigger a dependency failure,
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*>> so you cannot miss them.
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*>>
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*>> Best,
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*>> Jérôme
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*>>
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*>> On Wed, 13 Mar 2019 at 14:04, <yjcoshc_at_gmail.com
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*>> <mailto:yjcoshc_at_gmail.com>> wrote:
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*>>
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*>> Dear NAMD and Colvars developers,
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*>>
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*>> If I have a vector *v* = *R* * *X* - *X*_ref, where the *X*
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*>> is current Cartesian coordinates of a set of atoms, *X*_ref
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*>> is the reference coordinates and *R* is the optimal rotation
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*>> matrix, and in the C++ interface I have correctly setup the
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*>> ref_pos of atom_group *X* in the C++ interface. Assuming I
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*>> have a scalar function f(*v*) and I know the derivative of f
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*>> with respect of *v* (df/d*v*), can I use df/d*v *as the
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*>> atomic gradients of atom_group *X*? In other words, can I
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*>> assume d*R*/d*X* is automatically computed when I have setup
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*>> b_rotate and ref_pos of *X* in the atom_group initialization?
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*>>
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*>> Thanks,
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*>>
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*>> Haochuan Chen
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*>>
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*>>
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*>
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*>
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*> --
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*> Giacomo Fiorin
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*> Associate Professor of Research, Temple University, Philadelphia, PA
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*> Contractor, National Institutes of Health, Bethesda, MD
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*> http://goo.gl/Q3TBQU
*

*> https://github.com/giacomofiorin
*

**Next message:**Brian Radak: "Re: Re: Didn't Find vdw parameter QMMM"**Previous message:**Giacomo Fiorin: "Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly?"**In reply to:**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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