VMD-L Mailing List

From: Dudo (dudomail_at_gmail.com)
Date: Wed Sep 03 2014 - 02:00:12 CDT

well, you may want to determine what your typical angle is,
because although the energy minimum for a given potential could
be 120 deg but the equilibrium angle for the molecule may be different.
for this purpose you can calculate angular-radial distrubution map
and your actual bonding angles will be seen as a pattern of increased
occurence on the map.. for this you just need the double loop
as suggested earlier..

On Wed, Sep 3, 2014 at 8:21 AM, Pavan Miriyala <pavan.kumar9111_at_gmail.com>
wrote:

> thank you karthik and axel,
> Axel, I think I have not communicated the
> problem well, you are guiding me to find out angles when sheet has ideal
> bonds and angles using programming or permutations. But in my case, the
> ideal angle is 120, at the time step where crack propagation begins angles
> will be in the range of 80-140. how I guess it mathematically or
> programming ?
> I want to know exact thing happened in sheet.
> After trying few commands in the sense, not just trials :)
>
>
> Thanks & Regards,
> Venkata Pavan Kumar. Miriyala
> pavan.kumar9111_at_gmail.com,
> contact number: +91-9032307746
>
>
>
> On Tue, Sep 2, 2014 at 7:12 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
>> On Tue, Sep 2, 2014 at 2:11 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.
>>
>> you cannot learn these kind of things by just "trying a few commands"
>> and waiting for a perfect solution to drop down on you. programming
>> doesn't work like this and neither does research. you need to
>> think(!!!) about your problem and solve it in steps.
>>
>> what you are asking for is not rocket science and the process of
>> solving it yourself will also be highly educational and prepare you
>> for solving the next and more complicated problem.
>>
>> axel.
>>
>> >
>> >
>> > 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.
>>
>
> 

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