From: João Ribeiro KS (
Date: Thu Nov 17 2016 - 08:41:03 CST

Dear Jrhau,

Let me add some more information here. By the way, when checking the
simulation performance, check the days/ns in the simulation log file
created in the the "run" folder, inside the QwikMD output folder. This is
actually the value that you want to see decreasing.

In QwikMD, make sure that you are running the simulation in the background
and not with the Live View mode switched on. The Live View (Interactive MD
- IMD) significantly decreases NAMD performance. If you already created the
files, you just need to edit the file manually, changing the "IMDon on" to
"IMDon off".

Another values to consider are the energies printing frequency values,
which QwikMD sets to print very frequently by default. To decrease the
frequencies, please increase the values of outputenergies, outputtiming,
outputpressure in the NAMD configuration files located in the "run" folder.
You can also increase the coordinates saving frequency (dcdfreq). Make sure
that the printing frequencies are high enough for the measurements that you
want to perform.

You may also want to test the number of CPU cores that return the best
performance for your system size (assuming only one GPU card). Using all
the cores does not necessarily means the best performance.


On Thu, Nov 17, 2016 at 6:48 AM jrhau lung <> wrote:

> The answer is provided by the VMD CUDA accerlaterate note.
> Sorry for this question. and I would need another cheap graphic card.
> 2016-11-17 13:58 GMT+08:00 jrhau lung <>:
> Dear VMD friends:
> When running MD simulation using QwikMD, a low GPU usage (well below
> 30%) was found when checked by nvidia-smi -l command in terminal. Is this
> normal? Is there a way to improve the GPU usage and booster up the
> simulation?
> sincerely,
> Jrhau
> The following is the hardward and software in my computer.
> 1.VMD 1.9.3 beta 1 (LINUX_64 OpenGL, CUDA, TachyonL-OptiX
> <>
> )
> 2. NAMD 2.11 (Linux-x86_64-multicore-CUDA
> <>
> )
> 3. NVIDIA Linux driver (LINUX X64 (AMD64/EM64T) DISPLAY DRIVER 367.48)
> 4. Cuda 8.0 linux toolkit 14.04
> in Xeon E5-2670 + GTX970 desktop computer with OS=Ubuntu 16.04 LTS