VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 17 2010 - 14:41:03 CDT

I'm not a LAMMPS user, but I was under the impression that the LAMMPS
folks had some scripts to sort out these issues?
You might search the mailing lists (this one and LAMMPS) for such a script.
Otherwise, perhaps Axel or one of the other LAMMPS users can direct
you to a script or something you can use.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jun 15, 2010 at 04:44:58PM -0400, shiziyuan wrote:
> Dear All,
>
> I want to visualize my lammps trajectories results in VMD. But because of
> my results are from parallel computing, the number of atom is not arranged
> in an ordered way. So when I visualized my results by writing the script
> on vmd:
>
> vmd mywater.psf -lammpstrj dump.mywater
>
> I was able to visualize but the visualization is mixed up together.
>
> If I visualized results from running on just single processor which the
> atoms were listed in an ordered way, It's OK. But from parallel results,
> it's messed up.
>
> Can anybody give me some suggestion?
>
> Thanks!
>
> ziyuan 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078