## VMD-L Mailing List

**From:** Pavan Miriyala (*pavan.kumar9111_at_gmail.com*)

**Date:** Wed Sep 03 2014 - 10:23:12 CDT

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

No, even If I assign a variable with just integer, not a list. It is not

reading it as a integer

*>Main< (pavan) 97 % set a 1
*

1

*>Main< (pavan) 98 % set b 0
*

0

*>Main< (pavan) 99 % set c 5
*

5

*>Main< (pavan) 100 % measure angle $a $b $c
*

measure angle: must specify exactly three atoms in a list

*>Main< (pavan) 101 % measure angle { $a $b $c }
*

expected integer but got "$a" measure angle: bad atom index

*>Main< (pavan) 102 %
*

But this only works

*>Main< (pavan) 102 % measure angle {1 0 5}
*

120.00004577636719

Thanks & Regards,

Venkata Pavan Kumar. Miriyala

pavan.kumar9111_at_gmail.com,

contact number: +91-9032307746

On Wed, Sep 3, 2014 at 8:47 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

*> On Wed, Sep 3, 2014 at 5:14 PM, Pavan Miriyala
*

*> <pavan.kumar9111_at_gmail.com> wrote:
*

*> > Dear Axel,
*

*> > Thanks a lot :)
*

*> > I have taken data of all atoms forming angles in this form {1 0 5 } (
*

*> atoms
*

*> > 1,0,5 are forming angle).
*

*> > but can measure command works with variables?
*

*> >
*

*> > I'm getting an error:
*

*> >
*

*> >>Main< (pavan) 91 % set angl { {1 0 5} }
*

*> > {1 0 5}
*

*> >>Main< (pavan) 93 % measure angle $angl
*

*> > measure angle: must specify exactly three atoms in a list
*

*> >
*

*> > where as
*

*> >>Main< (pavan) 94 % measure angle {1 0 5}
*

*> > 120.00004577636719
*

*> >
*

*> > why it can't read variables ?
*

*>
*

*> this has nothing to do with variables. your variable contains a list,
*

*> but the command expects three individual numbers. that is different.
*

*> have another look or two into the Tcl tutorial on www.tcl.tk. these
*

*> are not VMD problems, but Tcl problems.
*

*>
*

*> axel.
*

*>
*

*>
*

*> >
*

*> >
*

*> >
*

*> > Thanks & Regards,
*

*> > Venkata Pavan Kumar. Miriyala
*

*> > pavan.kumar9111_at_gmail.com,
*

*> > contact number: +91-9032307746
*

*> >
*

*> >
*

*> >
*

*> > On Wed, Sep 3, 2014 at 3:35 PM, Pavan Miriyala <
*

*> pavan.kumar9111_at_gmail.com>
*

*> > wrote:
*

*> >>
*

*> >> Thank you axel
*

*> >>
*

*> >> Thanks & Regards,
*

*> >> Venkata Pavan Kumar. Miriyala
*

*> >> pavan.kumar9111_at_gmail.com,
*

*> >> contact number: +91-9032307746
*

*> >>
*

*> >>
*

*> >>
*

*> >> On Wed, Sep 3, 2014 at 1:37 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
*

*> wrote:
*

*> >>>
*

*> >>> 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.
*

*> >>
*

*> >>
*

*> >
*

*>
*

*>
*

*>
*

*> --
*

*> 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.
*

*>
*

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