Does the "namd-temp.namd" file exists in the path specified in the command?

Thank you for your answer, I checked and yes the file exists

As Martin Klvana said, this is a file i/o problem. Are you trying to execute namd in a different directory ? (maybe the namd setup is somewhere else)

You can add namd to your $PATH variable, so you can execute it freely without defining an absolute path.

Ali Osman Acar I will try, thank you !

Hi Judith Weber, did you manage to solve this? I'm getting the exact same error and adding namd to my PATH as Ali Osman Acar suggested unfortunately hasn't fixed it.

When I have this problem it is usually because the input file is not where NAMD is expecting it to be. My understanding is that NAMD expects the input file to be in the same directory where you executed the command to run NAMD, which for me is not the same directory where I have NAMD installed.

For your case I would inspect the contents of the variable $namdcmd (I assume this looks something like "/PathtoNAMDfolder/namd2 +auto-provision") and also check to see if "namd-temp.namd" is in the same directory where you are starting your "exec" command, if not cd to the directory where it is at and then execute.

However, based on your pasted output it looks like you have a few nested scripts for starting your NAMD runs which could complicate things and may make my suggestion incomplete.