Hello, I need help.
So I am trying to do this tutorial simulation: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/04_EM.html
and I'm calling files to gmx grompp to operate on with the following command:
# gmx grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/Methane/methane_water.gro -p $FREE_ENERGY/Methane/topol.top -o min$LAMBDA.tpr
... but gromacs is telling me that these files don't exist. I've created the em_steep* files with the perl script provided, copied and pasted the other files in the tutorial. I have checked all of these files, and these are not empty files and they do exist. There seems to be something wrong with the directory calling.
I've provided the error message file picture that I'm seeing in my terminal, and a directory tree calling to show that I have the files Gromacs states don't exist do exist.
Can you help me? Why is this happening?
You haven't set $FREE_ENERGY or $MDP so grompp returns null as its value and it is literally looking for /EM/ and /Methane/ be the top-level directories (i.e. from the root level). Also note that your variable substitution is not working because it is looking for em_steep_.mdp instead of the properly named file that includes its index.
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