VMD-L Mailing List

From: Pavan Miriyala (pavan.kumar9111_at_gmail.com)
Date: Wed Sep 03 2014 - 02:08:45 CDT

Yes exactly, thank you :) , using restart file, rerunning it can give
information. but using many body potential is it possible? Please give me
some references in literature or any examples.

Thanks & Regards,
Venkata Pavan Kumar. Miriyala
pavan.kumar9111_at_gmail.com,
contact number: +91-9032307746

On Wed, Sep 3, 2014 at 12:30 PM, Dudo <dudomail_at_gmail.com> wrote:

> 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.
>>>
>>
>>
>
>
> --
> ____________________
> Ing. Dusan Racko, PhD
> https://www.researchgate.net/profile/Dusan_Racko
> Polymer Institute of the Slovak Academy of Sciences
> Dubravska cesta 3
> 845 41 Bratislava, Slovak Republic
> tel: +421 2 3229 4321
>