Looping

The Unix programming paradigm can also allow for programming technqiues like looping, which allows for more complex scripts that extend beyond a single line.

Conditionals, loops, and job control:

1. Conditional statements: run commands only when some condition is met

   if [ -f dir/file ]; then echo "file found"; fi
   if [ -d dir ]; then echo "dir found"; fi
   

2. Looping: repeat commands

   for i in {1..10}; do echo -n "$i "; done
   while read -r line; do echo "$line"; done < file
   

3. Job control: run commands in the background

   script.sh &
   top
   kill pid
   pgrep -a vmd
   pkill -9 vmd
   

Exercise:

Create a script that could help you do your research more efficiently! Have it run a simulation in parts, and figure out which part you have already run by checking for existing output or checkpoint files. You may want to start with iterations of identical production runs, or build up a minimization > equilibration > production script.

Note: CHARMM-GUI generates these files, but as csh not bash scripts. You could get ideas from their code, but you will need to “translate” certain c-shell syntax ideas to bash.