VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Sep 02 2014 - 08:37:31 CDT

On Tue, Sep 2, 2014 at 3:08 PM, karthik kumar <karthik3327_at_gmail.com> wrote:
> Write a simple TCL script which loop over the indices of all the atoms in
> a molecule
>
> If N is the total number of atoms
>
> TCL script look like this
>
>
> for ( i=0 ; i< N -2 ; i++ )
>
> measure angle i,i+1,i+2

no. that is not a good suggestion. that will only find a subset and
may not find actual real angles.

if there is only information about atoms, one first needs to determine
the bonds (based on suitable criteria) and, if needed bonds that cross
periodic boundaries (VMD doesn't "find" them by default) and from
those bonds one can fairly easily reconstruct all topological angles,
since those are all permutations of pairs of bonds that share one atom
(only).

>
>
>
> Karteek
>
>
>
>
>
> On Tue, Sep 2, 2014 at 5:41 PM, Pavan Miriyala <pavan.kumar9111_at_gmail.com>
> wrote:
>>
>> Dear Axel,
>> just like topo getanglelist, can we measure all the angles
>> in the molecule with out specifying three atoms using measure command.
>> Sorry, for disturbing you I have gone through the vmd user's guide and tried
>> few commands.
>>
>>
>> Thanks & Regards,
>> Venkata Pavan Kumar. Miriyala
>> pavan.kumar9111_at_gmail.com,
>> contact number: +91-9032307746
>>
>>
>>
>> On Mon, Sep 1, 2014 at 6:49 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>>
>>> On Mon, Sep 1, 2014 at 2:36 PM, Pavan Miriyala
>>> <pavan.kumar9111_at_gmail.com> wrote:
>>> > Dear all,
>>> > How can we get bond angles and bond length distribution using
>>> > VMD
>>> > through lammps xyz trajectories. Is there any processing extension for
>>> > getting distribution of bond angles and lengths all over the sheet.
>>>
>>> i already answered your question on the LAMMPS mailing list.
>>>
>>> >
>>> > Thanking you
>>> >
>>>
>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.