From: yjcoshc (yjcoshc_at_gmail.com)
Date: Wed Mar 15 2017 - 08:39:58 CDT
Thanks for your reply!
Best,
yjcoshc
在 2017/3/15 20:26, Jérôme Hénin 写道:
> Hi yjcoshc,
>
> Does that means the oneSiteTotalForce option only affect the
> measurement of the forces and doesn't have effect when applying
> the forces to atoms?
>
> That is correct.
>
> If two colvars have overlapping atoms and they apply the bias
> forces to their common atoms, are these two colvars still mutual
> orthogonality?
>
> Yes, as long as they don't measure forces on those common atoms. The
> exact requirement is that the gradient of one variable is orthogonal
> to the inverse gradient of the other [1], or equivalently, that
> biasing forces on one variable are orthogonal to the force measurement
> on the other.
> Best,
> Jerome
>
> [1] Exploring Multidimensional Free Energy Landscapes Using
> Time-Dependent Biases on Collective Variables, J. Chem. Theory
> Comput., 2010, 6 (1), pp 35–47
> http://pubs.acs.org/doi/abs/10.1021/ct9004432
>
> On 15 March 2017 at 13:11, yjcoshc <yjcoshc_at_gmail.com
> <mailto:yjcoshc_at_gmail.com>> wrote:
>
> Dear All,
>
> I am confused about the orthogonality of colvars and the
> oneSiteTotalForce option in the user guide. The user guide says:
>
> atoms involved in the force measurement on i do not participate
> in the definition of j . This can be obtained using the option
> oneSiteTotalForce of the distance, angle, and dihedral components
> (example: Ramachandran angles , ).
>
> Does that means the oneSiteTotalForce option only affect the
> measurement of the forces and doesn't have effect when applying
> the forces to atoms?
> If two colvars have overlapping atoms and they apply the bias
> forces to their common atoms, are these two colvars still mutual
> orthogonality?
>
> Thanks,
> yjcoshc
>
>
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