Re: Dihedral definition in NAMD

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Mar 10 2015 - 09:33:15 CDT

Kevin, you may want to try colvars inside VMD, calculating the variables
without starting NAMD.

I would recommend that you download and compile the source code of VMD,
updating it with the colvars code from Github using the provided
update-colvars-code.sh script:

https://github.com/colvars/colvars/archive/master.zip

Giacomo

On Tue, Mar 10, 2015 at 3:24 PM, Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk>
wrote:

> 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.
>
> Thanks in advance,
> 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?
>
>
> ​Thanks, in advance,
> 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/
>>
>>
>
>
>

-- 
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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