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