Re: Dihedral definition in NAMD

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Mar 10 2015 - 18:46:42 CDT

Hi Kevin, I think you will probably need:
puts [cv colvar dih value]
to see the value printed on the screen. Think of that command between
brackets as a measure command.

You would need to recompile VMD if you load in multiple configurations
files. What you're using there should be fine with 1.9.2

On Tue, Mar 10, 2015 at 7:13 PM, Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk>
wrote:

> Thanks to all of you and your replies. I got vmd1.9.2 and cv works
> horribly well.
>
> ***Except*** that I found my “cv” (shipped with
> vmd1.9.2-linux-opengl-cuda) just cannot run inside a for-loop:
> # I have loaded a number of frames and wanna compare their colvar values #
> cv molid top
> cv configfile dih.colvar
>
> for { set i 0 } { $i <= 9 } { incr i } {
> cv frame $i
> cv colvar dih update
> cv colvar dih value
> }
>
> By "cannot run" it means the vmd did not either give error messages or
> quit, instead just nothing happens.
>
> I noticed that Giacomo had given an update of colvars from Github but it
> seems I have to build my VMD from the source files especially all those
> libraries. I am just asking whether the update solves my problem of
> not-working-in-a-loop. If yes, I will go back and compile it. If no, what
> is it about actually?
>
> Thanks in advance,
> Kevin
>
> On 10 Mar, 2015, at 22:33, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
> 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/
>
>
>

-- 
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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