VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Mon Nov 20 2023 - 22:30:15 CST

Hi Fred,
I must agree with Josh, 500k particles should not be an issue for VMD
to represent as Lines.
If it is not RAM or issues with nvidia-drivers, can you try the following?

Extensions->Modelling->Add Solvation Box. Mark on "WaterBox only" and make
a 200x200x200 box.
It should give you >700k atoms, and rotate smoothly. I tried a 300^3 box
with 2.6 million atoms that rotates smoothly on my laptop (M1 mac).

Please let us know if that doesn't work.

Friendly,
Diego.

On Mon, Nov 20, 2023 at 10:41 AM Vermaas, Josh <vermaasj_at_msu.edu> wrote:

> 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.
>
>
>
> -Josh
>
>
>
> *From: *<owner-vmd-l_at_ks.uiuc.edu> on behalf of Frederico De Santana
> Pontes <F.Pontes_at_leeds.ac.uk>
> *Date: *Monday, November 20, 2023 at 8:03 AM
> *To: *"vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> *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
>
> NVIDIA T1000/PCle/SSE2
>
> 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,
>
>
>
> Fred
>
>
> 

-- 
Diego Enry B. Gomes, PhD
Department of Physics at Auburn University &
NIH Center for Macromolecular Modeling and Visualization
Leach Science Center - Ste. 3182 - Auburn, AL
dgomes_at_auburn.edu