From: Axel Kohlmeyer (
Date: Fri Jan 23 2009 - 16:20:30 CST

On Thu, 22 Jan 2009, Iman Salehinia wrote:

dear iman,

IS> Dear John,
IS> One of my friends using VMD had a problem for his modeling. The number of
IS> atoms in his model is about 1000000 and VMD didn't work with this amount of
IS> atoms (his memory is 4 GB). Will this problem be solved in the new version

the big question is whether this is a problem of
VMD or rather how it is being used, or in which

VMD is not visualization snake oil. at some point
you have to make decisions of how to handle certain
problems and what would be the better solution.
developers of different tools make different choices
and thus their tools are more or less suited for
a specific problem. that being said, the memory
footprint of VMD for use with large systems has
been systematically reduced over time.

IS> of VMD? AtomEye doesn't have this problem, so this problem really forces
IS> anyone to not to work with VMD, actually when the number of atoms is big!

no, you can use VMD with systems far larger.

regardless of that, have you or your friend actually
_reported_ the problem and provided some example
that _demonstrates_ the problem at hand? so that
it can be reproduced, identified and treated.
rather than claiming (without giving any proof!)
that something doesn't work, it would be better
to help people to find the cause.

since you mention atom eye and large systems, could it
be by any chance that your friend is using LAMMPS and
is trying to read text format lammps trajectory files?


IS> Regards,
IS> Iman.

Axel Kohlmeyer
   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