From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Mar 10 2015 - 13:32:12 CDT
Hi Kevin,
Here is an example of how I use colvars in VMD, when I was calculating a
tiltangle:
colvars molid $mid
colvars configfile ../Analysis/tiltcolvar.conf
foreach dcd $dcdlist {
mol addfile $dcd waitfor all molid $mid
for { set i 0 } { $i < [molinfo $mid get numframes]} { incr i } {
colvars frame $i
colvars update
puts $fout "$counter [colvars colvar cosangle value]"
incr counter
}
animate delete all
}
colvars delete
The major difference is that cv colvar dih update doesn't work like its
supposed to in VMD 1.9.2.
-Josh
On 03/10/2015 01:13 PM, Kevin C Chan 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
>> <mailto: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 <mailto: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
>>> <mailto: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 <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
>>>> 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), 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 <tel:%2B1-215-204-4213>
>>>> 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 <tel:%2B1-215-204-4213>
>> https://icms.cst.temple.edu/members.html
>> http://giacomofiorin.github.io/
>>
>
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:42 CST