VMD-L Mailing List

From: Pavan Miriyala (pavan.kumar9111_at_gmail.com)
Date: Wed Sep 03 2014 - 05:05:03 CDT

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.
>