I am writing a Bash script that runs a command-line program (Gromacs), saves the results, modifies the input files, and then loops through the process again.
I am trying
You can script Vim via the -c flag.
vim -c "set ff=dos" -c wq mine.mak
However that only gets you so far.
:normal. e.g. :norm ddcommands.vim) and then :source via -S.:h ex-cmd-indexSo you will end up with something like this. With all your Vim commands inside of commands.vim.
vim -S commands.vim mine.mak
You may also want to look into using sed and/or awk for text processing.