Re: Dihedral definition in NAMD

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Tue Mar 10 2015 - 09:24:23 CDT

Thanks Josh!

I am also wondering whether we can calculate such dihedral of 4 groups simply using pdb+psf. Because right now I am doing with colvars turned on and running few steps of a random MD and look at the colvars.traj and honestly it is as stupid as it sounds.

Kevin
> On 10 Mar, 2015, at 22:14, Josh Vermaas <vermaas2_at_illinois.edu> wrote:
>
> Hi Kevin,
>
> I believe the way it is written is pretty standard, using the ordering that folks use to describe dihedral potentials within molecules, and just generalizing it to groups of atoms. So group1 would be first atom, group2 would be the second, and so on. The "dihedral" angle is measuring rotation around the group2-group3 "bond" by measuring the angle between group1 and group4 if you are looking down the group2-group3 bond (Fig. 3 from the Wikipedia article).
>
> -Josh Vermaas
>
> On 03/10/2015 06:52 AM, Kevin C Chan wrote:
>> 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 <mailto: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 <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 <mailto: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 <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?
>>
>>
>> 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