VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Feb 15 2008 - 16:51:34 CST

On Fri, 15 Feb 2008, Arnab Chakrabarty wrote:

AC> Hi,
AC> I am using a LAMMPS dump file in VMD 1.8.6 version in Mac
AC> 10.4.11version. While the Lines representation works ok, when i try to
AC> change it to
AC> VDW or CPK representation it just shows some dots. I am not sure why
AC> this is happening. The console gave the following message

AC>
AC> 'RCNE SendEventToEventTarget (suom Moved ) failed, -50'

this seems to be harmless and X-server related.
 
AC> I looked through the some of the messages in mailing list which for
AC> similar error messages with a different action seems not to do with
AC> file format. Any help is appreciated.

the problem is with the LAMMPS dump file format not containing
any useful information about the atom types (just numbers 1,2,3
and so on). so you have no elements and thus no radius.

if you have a .pdb/.psf of the system (or can create one)
you could load that file first and then the lammps dump
(but in that case you would also be better off with .dcd
or .xtc as they are binary and thus smaller and faster to read).

what i usually do is to load one frame of the lammps dump,
and then create a selection for each atom type and then
set the relevant properties. for model systems, that do
not related to any real atoms, i actually have a small
script that i do execute after loading the parses that
information from a lammps data file and assigns it automatically.

cheers,
   axel.

AC>
AC> Thanks
AC> Arnab
AC> 

-- 
=======================================================================
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.