VMD-L Mailing List

From: shiziyuan (shiziyuan1124_at_gmail.com)
Date: Thu Jun 17 2010 - 15:44:41 CDT

yes. thanks very much.

ziyuan

On Thu, Jun 17, 2010 at 4:34 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> john,
>
> 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.
>
> cheers,
> axel.
>
> On Thu, Jun 17, 2010 at 3:41 PM, John Stone <johns_at_ks.uiuc.edu> 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
> > 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
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>