From: Axel Kohlmeyer (
Date: Fri Sep 17 2010 - 12:35:27 CDT

On Fri, Sep 17, 2010 at 12:43 PM, Ramasamy, Ellankavi
<> wrote:
> Hello,
> I have a rather large PDB file with more than 4million atoms.
> I have an Intel Core 2 quad processor with 2.83GHz,  an nVidia Geforce GT 240 GPU with 1GB GRAM
> The rendering of the atoms is slow when compared to another computer that has much lesser processing power both in terms of CPU and GPU.

> I came across a post that said that for larger atom structures, it is better to shift from a text-based PDB file to a binary file that could be read by
> VMD much faster.

rendering and reading are two different issues.

if your graphics performance is bad, that your
xserver may be misconfigured or you may not
be using the best driver. for nvidia GPUs there
is the open source driver that ships with distributions
and the binary-only driver from nvidia. the latter
has much higher OpenGL performance.

if you send the output that VMD prints on startup
to the list, perhaps there is an indication what is wrong.


> How can I accomplish this?

catdcd can convert files.
> Thanks
> Ellankavi Ramasamy
> Institut für Materialprüfung, Werkstoffkunde und Festigkeitslehre
> Universität Stuttgart
> Deutschland

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