From: Axel Kohlmeyer (
Date: Thu Jun 17 2010 - 15:34:31 CDT


this question has been solved on the lammps list.
there is an open issue in matching that generated
psf to the native lammps trajectory file format that i
have to take care of at some point.


On Thu, Jun 17, 2010 at 3:41 PM, John Stone <> wrote:
> 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
> 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:                 Phone: 217-244-3349
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Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.