From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Tue Mar 10 2015 - 06:52:53 CDT
Thank you so much for the hint from "distance".
Concerning the dihedral definition, I am not sure whether I get what you
are saying. In the Wikipedia, under the section "Dihedral angles of four
, it uses words like first atom, second atom and so on, so is this the
sequence that NAMD colvars are using for dihedral calculation?
Thanks, in advance,
On Tue, Mar 10, 2015 at 7:28 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> The center of mass is not mentioned explicitly for all components, but
> these are all consistent with the distance:
> 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
> 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,
>> 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
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