VMD-L Mailing List

From: Nima Nouri (nouri.f.nima_at_gmail.com)
Date: Thu Jul 21 2011 - 18:41:05 CDT

On Fri, Jul 22, 2011 at 4:04 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> > Thanks a lot Dr. Kohlmeyer
> > the information was really helpfull. However, now I have another
> question.
> > how is it possible to use the trajectory output > user coloring in the
> VMD.
>
> please always cc the mailing list for additional queries
> of followup questions. thanks.
>
OK, I will.

>
>
> I mean if i am going to write an output file containing the virial tensor
> in
> > adition to the trajectory and visualize it by color on the particles.
>
> a virial tensor contains independent 6 numbers,
> how are you going to map it to a single color?
>
>
>
There are a lot of ways like von-mises equivalent stress but
I want one of them each time.

>
>
> Do you propose a better way for coloring the atoms with regard to the
> virial
> > tensor using present output formats or I should try to output a in-house
> > formatted output and write a vmd script for it.
>
> the recommended alternative would indeed be writing out
> the data so that it can be read in conveniently through VMD
> scripting. some examples are presented in the pdf attached here:
> http://sites.google.com/site/akohlmey/redirect
>
>
>
Thanks, The PDF was great.

> >
> > A million thanks in advance.
>
> a single one will do.
>
But this is the only thing I can give you.

>
> cheers,
> axel.
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
> 

-- 
Best Regards
N.Nouri
Ph.D Student
Department of Mechanical Engineering
Isfahan University of Technology
Isfahan, Iran