Re: dihedral colvar

From: Stefano Guglielmo (stefano.guglielmo_at_unito.it)
Date: Wed Jan 18 2017 - 01:43:48 CST

Thanks for your suggestions, I will go through that. Actually what I meant
is the torsional generateed by the two principal axes and the segment
connecting their origins but I was too short.

Thanks again

2017-01-18 3:47 GMT+01:00 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>:

> What you describe can't be a torsional angle, unless you define an
> additional axis to represent the line where the two hypersurfaces (planes)
> intersect.
>
> You can, however, compute the angle of the quasi-rigid rotation (e.g.
> orientationAngle for the small-molecule ligand) in a rotated frame that
> is defined by the protein as fittingGroup. There is an example for the
> use of fittingGroup here:
> https://github.com/colvars/colvars/blob/master/examples/
> 07_permeation.colvars.in
>
> For proteins, this is also numerically more stable than computing the
> inertia eigenvectors because the identity of the atoms is tracked by doing
> the same optimal alignment done in computing minimal RMSD.
>
> For more details, please read the doc:
> http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html
>
> On Tue, Jan 17, 2017 at 8:11 PM, Stefano Guglielmo <
> stefano.guglielmo_at_unito.it> wrote:
>
>> Dear NAMD users, is it possible to define a collective variable as a
>> torsional angle between the principal axes of two molecules in a
>> protein-ligand system?
>>
>> Thanks in advance
>> Stefano.
>>
>> --
>> Stefano GUGLIELMO PhD
>> Assistant Professor of Medicinal Chemistry
>> Department of Drug Science and Technology
>> Via P. Giuria 9
>> 10125 Turin, ITALY
>> ph. +39 (0)11 6707678
>>
>>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213 <(215)%20204-4213>
>
> Scholar: http://goo.gl/Q3TBQU
> Personal: http://giacomofiorin.github.io/
> Lab page: https://icms.cst.temple.edu/members.html
>
> *"As computer programmers we have a responsibility to make sure that we
> run the computers instead of the computers running us."* - Steve Oualline
>
>
>

-- 
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707678

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