Error with "namd"

From: Bob Masong (
Date: Wed Oct 26 2011 - 00:01:21 CDT

Hello NAMD community,

I tried to run the first simulation as specified in the tutorial, I was able to generate all the necessary files without any errors. But after Section 1.4.2 in the "namd-tutorial.pdf".
I have some questions and I'm open to all answers.
1. I tried to run the simulation after moving to 1-2-sphere directory of the namd-tutorial-files directory.
> cd namd-tut/1-2-sphere
> namd-tut/1-2-sphere ./namd2 ubq ws eq.conf > ubq ws eq.log & ( I received a run aborted message in the terminal. I would include it in the message but I don't have the output right now.)
2. If I have an Nvidia GPU card that I believe is capable of being the CUDA-accelerator. But I'm not sure if it will work.
It's an Nvidia GT430 card. It's used as the primary video card for my Ubuntu system.
Following the directions in the NAMD user manual I tried to run the simulation using this line: "
                  ./namd2 +idlepoll ubq ws eq.conf > ubq ws eq.log &
This also resulted in an error. In the terminal window the error message pointed out that the CUDA-accelerator was "prohibited" from being used. So far I think there are two possible explanations: NAMD will only use a CUDA accelerator that is not being used by X-server OR I am not including a statement that would allow namd to use the video card.

3. I noticed that in the directory "1-2-sphere" there exist an executable file named "namd2" this is also true for the CUDA-version of NAMD2.8 that I downloaded. Is it safe to use the executable "namd2" alredy in the directory or am I supposed to replace this file with the executable packaged in the "namd2.8-Linux-x86_64-CUDA.tar.gz" that I downloaded?

4. The namd user manual says to include in the LD_LIBRARY_PATH. How do I do this?

Lastly, does anyone know how NAMD runs on the new corei7 sand bridge 2600K processor as compared to other processors. (All inputs welcome)

Many Thanks,

Bob M.

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