I am doing a molecular dynamics simulation on PBS cluster. I wrote a run.sh script for sander command for PBS. However it turns out that as soon as I submit it via qsub run.sh, the qstat shows it for a moment and then no more. There are no output files in the current directory and no error message. However, there is an mdout file in my home directory on cluster which has the error message : Error opening unit 5: File "polyAT_wat_md_heat.in" is missing or unreadable
However when I run the same sander command in command line instead of script, it works perfectly does MD and generates all the required output files. I am not sure what is wrong with my system?
It seems the input file is not in the directory where you are submitting or running your jobs.
Supriyo Naskar .. It is. Otherwise sander from command-line shouldn't have run properly either. Also, the exact same steps I use now used to work fine few days back.
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