## VMD-L Mailing List

**From:** Axel Kohlmeyer (*akohlmey_at_gmail.com*)

**Date:** Wed Sep 03 2014 - 03:07:04 CDT

**Next message:**Pavan Miriyala: "Re: How to get all bond angles and bond distances for all atoms in sheet"**Previous message:**Pavan Miriyala: "Re: How to get all bond angles and bond distances for all atoms in sheet"**In reply to:**Pavan Miriyala: "Re: How to get all bond angles and bond distances for all atoms in sheet"**Next in thread:**Pavan Miriyala: "Re: How to get all bond angles and bond distances for all atoms in sheet"**Reply:**Pavan Miriyala: "Re: How to get all bond angles and bond distances for all atoms in sheet"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

On Wed, Sep 3, 2014 at 9:08 AM, Pavan Miriyala

<pavan.kumar9111_at_gmail.com> wrote:

*> 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.
*

i already mentioned to you twice, what you need to do. you obviously

have locked in you mind a certain thing that you believe that you need

to do and a certain way how it would work. but it an very convinced

that you are looking at the problem from the wrong angle and thus are

desperately trying something that will lead nowhere. the issue is that

you refuse to see that your problem needs to be solved in multiple

steps. i am outlining them one more time.

what you need to do is to determine all "topological angles" (in the

way i explained before), that is you need to identify all atom

triplets that you want to compute the angle of, i.e. those where two

bonds share an atom. since you also don't have the bonds, you need to

determine them as well (e.g. based on a distance guess). this is

extremely similar to what needs to be done for building a topology for

a "regular" force field. it doesn't matter that you are using a

manybody potential, you do not need to use that topology for your

simulation, only for analysis.

and as explained before, that can be used with LAMMPS using "rerun"

and than can be used with VMD using measure or with a standalone

postprocessing program. only there is not one single command, one

single tool that will do it right away. you do have to write a

script/program that systematically does all the steps and then

collects the information you need (by looping over the topological

angle triples) and creating the histograms from it.

this really isn't a complicated operation and people are doing similar

things all the time (a lot of the VMD script library and plugins

started like that).

in the end, the problem you are facing is not really a problem of the

science of your task, but simply an issue that you need to have a

better strategy to solve a problem. common problems can be solved by

reusing a solution that somebody else provided, but anything beyond

that has to be solved by yourself and the best way to solve a complex

problem is to break it down into smaller more easily solvable

problems.

i have outlined such a strategy for you multiple times already. short

sitting down myself and writing such a script for you (you need to

contract me for that), that is all i can do.

since you ask for literature. here is my favorite book on that topic.

http://www.nostarch.com/thinklikeaprogrammer

axel.

*>
*

*> 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
*

*>
*

*>
*

-- 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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