From: Axel Kohlmeyer (
Date: Thu Aug 12 2010 - 18:20:52 CDT

On Thu, Aug 12, 2010 at 5:58 AM, Cun Zhang <> wrote:
> It is a cvs version.  1.88.a7(August 9,2010)

hmmm... it looks like you compiled recently,
but didn't update the sources and didn't
rerun configure...

in any case, i think i tracked down the origin of the problem.
the "problem" is in the lammps trajectory reader. it was implemented
to sort the atom indices as i claimed, but that would only work
for systems where the atom indices are consecutive and start
from 1, so i added a hashtable to make sure that the order of
atoms in multiple frames was restored when reading. yet, that
code broke when sorting atoms by their id and since it was
briefly before the release of 1.8.7, the sorting was disabled.

i have looked at the code again today and found a way to restore
the sorting by atom index that does not break the hash table.

the code to build the plugin (only) is now uploaded at:

i will update the VMD cvs code next so that the updated
version should be in the public cvs by tomorrow morning
(US time).

please give it a try and let me know if it fixes your problems.


> Thank you!
> Cun Zhang
> More information as follows:
> cunzhang_at_Debian:~$ vmd
> Info) VMD for LINUXAMD64, version 1.8.8a7 (August 9, 2010)
> Info)
> Info) Email questions and bug reports to
> Info) Please include this reference in published work using VMD:
> Info)    Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info)    Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 4 CPUs detected.
> Info) Free system memory: 2563MB (64%)
> Info) Detected 1 available CUDA accelerator:
> Info)   [0] GeForce 9600 GSO   12 SM_1.1 @ 1.38 GHz,  511MB RAM, KTO, OIO
> Info) Creating CUDA device pool and initializing hardware...
> Info) OpenGL renderer: GeForce 9600 GSO/PCI/SSE2
> Info)   Full GLSL rendering mode is available.
> Info)   Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
> vmd > exit
> Info) VMD for LINUXAMD64, version 1.8.8a7 (August 9, 2010)
> Info) Exiting normally.
> On Thu, Aug 12, 2010 at 5:52 PM, Axel Kohlmeyer <> wrote:
>> can you please tell us which version of VMD you are using?
>> thanks,
>>     axel.
> Blog:

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.