From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Sep 08 2017 - 08:53:28 CDT
The cv command is available both in NAMD and VMD, once you've enabled the
colvars module.
You cannot use Tcl scripting within a colvars configuration file - you can
use it in the NAMD config file to generate colvars configuration strings as
in the example I gave above.
Jerome
On 8 September 2017 at 15:44, PRITI ROY <priitii.roy_at_gmail.com> wrote:
> Dear Jerome,
>
> Thank you for your fast reply. According to your script the "cv" command
> is accesible in vmd as per I know or I might be completely not understand
> well. If possible give some insights.
> I have written one tcl colvar configuration file using four types atom
> index which were saved in ".dat" file and run in loop. But when I run this,
> error shoing that "keyword "set" is not supported". Does "tcl" not
> accessible to colvar?
>
> Kindly enlighten this matter.
>
> Best,
> Priti
>
>
> On Mon, Sep 4, 2017 at 6:10 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>
>> Hi Priti,
>>
>> If I understand you correctly, you want to define a series of 50 dihedral
>> restraints. You will need to define one separate colvar for each angle, but
>> you don't have to write them separately. That can be scripted using a Tcl
>> loop:
>>
>> for {set i 0} { $i < 50 } {incr i} {
>> cv config "colvar { dihedral ... }"
>> }
>>
>> Where the colvar block contains the details of the dihedral angle. You
>> can use variable $i inside the block to define the specifics of each angle.
>>
>> Best,
>> Jerome
>>
>> On 4 September 2017 at 13:08, PRITI ROY <priitii.roy_at_gmail.com> wrote:
>>
>>> Dear all,
>>>
>>> I would like to do dihedral restrain using the colvar module of nearly
>>> 50 residues. I have gone through the colvar module. In dihedral colvar,
>>> there are four group selection which are for atoms and depending on 1st
>>> group it denote the particular dihedral angel. Basically this module
>>> describe in light of atoms.
>>>
>>> How could I define this dihedral colvar for residues?
>>>
>>> Please give some idea to resolve my problem.
>>>
>>> Thanks,
>>> Priti
>>>
>>
>>
>
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