Re: Run NAMD binaries

From: Axel Kohlmeyer (
Date: Wed Aug 29 2012 - 04:30:20 CDT

On Wed, Aug 29, 2012 at 10:58 AM, Monika Madhavi
<> wrote:
> Dear all,
> This is a very basic question but this is my first program in NAMD. I
> downloaded NAMD_2.9_Linux-x86 binary and extracted it in my home directory.
> My configuration file is also in the home directory. Then I typed namd2
> myconfigfile.conf in a terminal window and I got "namd2 command not found ".

this is not a NAMD issue at all, but a generic linux/unix issue.

unlike on some other operating systems, the current directory '.'
is not in the search path for executables, hence the error message
that 'namd2' is not found as a command.

you either have to add the directory with the NAMD executable
to your PATH environment variable, or use ./namd2 which will
use for the exectutable namd2 explicitly in the local directory.

have a look around the web for some tutorials on linux shell
basics. there are some really good ones around. that'll should
be also helpful to understand a lot of other things that you will
encounter in the future.


> Then I copied my configuration file inside the extracted folder and typed
> the same in terminal and got the same massage.
> Can someone please help me to find where I went wrong? Do I have to keep my
> configuration file in a specific location for namd to run it?
> Thank you.
> Monika

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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