From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Mar 10 2015 - 06:28:26 CDT
The center of mass is not mentioned explicitly for all components, but
these are all consistent with the distance:
http://www.ks.uiuc.edu/Research/namd/2.10/ug/node57.html#SECTION000134110000000000000
i.e. the groups' centers-of-mass are used to define individual points.
The only occasion where centers of geometry are used is for rotational fits.
Regarding the dihedral definition, how about taking a look at Figure 2 in
the same Wikipedia article?
On Tue, Mar 10, 2015 at 12:19 PM, Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk>
wrote:
> Dear Users,
>
> I am now trying to harmonically restraint a dihedral angle of four
> selections of atoms using colvar for a regular NPT simulation. However the
> colvar manual does not give clearly how it defined the dihedral angle from
> the 4 groups.
>
> For example, referring to figure 3 at wiki (
> http://en.wikipedia.org/wiki/Dihedral_angle), does a sequence - group 1 2
> 3 4 means that group 2 and 3 are overlapped and angle between b1(1-2) and
> b2(4-3) is measured?
>
> Also, how actually does the colvar treat a selection of atom when
> calculating the distances or angles? Is it using the center of mass or
> center of geometry?
>
> Thanks in advance,
>
> Kevin
> City University of Hong Kong
>
-- Giacomo Fiorin Assistant 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 https://icms.cst.temple.edu/members.html http://giacomofiorin.github.io/
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