VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu May 07 2009 - 21:22:51 CDT

On Fri, 2009-05-08 at 09:26 +0800, H Q wrote:
> hello, when i use lammps data, the error said :" Error while reading
> structure from lammps dump file' dump.atom' atomid 2878 is not in
> valid range [1 .1877]" "Error) ,molecule_structure: unable to read
> structure for molecule 0" I think this because when i dump data from
> lammps ,i just dump some group atoms ,not all atoms, and so atomid is
> not from 1 to 2788,but begin from other to other. how to do ? thank
> you.

the lammps dump reader in VMD has some limitations, several of them
will be lifted in the next beta or snapshot version of VMD. most of
the changes, however, require that you update to the latest patchlevel
of LAMMPS to have the full flexibility.

at the moment, you have to post process the file with, e.g., pizza.py
to some format that VMD can handle better.

cheers,
   axel.
>
>
> --
> shanghai 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.