From: Vermaas, Josh (
Date: Mon Nov 20 2023 - 08:57:13 CST

Hi Fred,

How many frames do you have loaded when this happens? 500k particles really isn’t that much to be drawing lines for normally, although some have more bonds drawn than others. I think there are two possibilities:

  1. Under RAM pressure (like when you have a lot of trajectory loaded), many linux systems are set up to use hard drive space as swap. This is terrible for performance, as the latency for most hard drives is much higher than RAM. You can check this pretty easily with “top” to see how much memory you still have available.
  2. Are you *sure* you are using NVIDIA drivers? Does “nvidia-smi” return something sane? Admittedly a T1000 is on the older side, but if you are using the open-source NVIDIA drivers, you will have a bad time in OpenGL applications.


From: <> on behalf of Frederico De Santana Pontes <>
Date: Monday, November 20, 2023 at 8:03 AM
To: "" <>
Subject: vmd-l: How to evaluate VMD performance properly?

Hi everyone!

I have some difficulties to work with VMD 1.9.3 on my machine. Rotating a system (~500k Coarse-grain beads)in a default configuration (Coloring Method: Name; Drawing Method: Lines; Material: Opaque) is a really hard task.

I know that my system is quite large, but I'm running VMD locally and my machine has the following features:

OS: Red Hat Enterprise Linux 8.8
Memory: 62.3 GiB
Processor Intel Xeon(R) W-2245 CPU @ 3.90 GHz x 16
GNOME v.3.32.2

I don't know if the difficulties to manipulate/rotate my system in VMD is due to the size system or some other reason, which I could improve on a new installation. Maybe I could make some tests to evaluate VMD performance, but I don't know which kind of test.
Someone could help me in this situation?

Kind regards,