From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Mar 10 2015 - 09:49:00 CDT
Sorry, I need to correct Josh: the command is "cv" (we chose that for
consistency with NAMD, that has the equivalent command in its own Tcl
interpreter).
There is also a small glitch in the colvars version shipped with VMD 1.9.2
that shows up when executing multiple "cv config" or "cv configfile"
commands. Sorry about that.
There is no issue if you us a single configuration file (as usually done in
NAMD prior to the new "cv" command) or compile the latest version of VMD.
Giacomo
On Tue, Mar 10, 2015 at 3:30 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:
> Hi Kevin,
>
> With VMD 1.9.2, you can! Colvars is built-in (open up a tkconsole, type in
> "colvars", and get started!), and no MD is required. It even reads standard
> colvar configuration files. Just be sure to call colvars update before
> asking for the value, since otherwise it will return 0.
> -Josh
>
>
> On 03/10/2015 09:24 AM, Kevin C Chan 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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