# Re: Dihedral definition in NAMD

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
atoms
​"
, it uses words like first atom, second atom and so on, so is this the
sequence that NAMD colvars are using for dihedral calculation?

Kevin​

On Tue, Mar 10, 2015 at 7:28 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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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