Linux Command Reference

Navigation

Command	What it does
pwd	Print the current directory
cd my_project/	Change into a directory
cd ..	Go up one directory
ls	List files
ls -la	List files, including hidden ones, with details

Files and directories

Command	What it does
mkdir simulation_01	Create a directory
touch notes.txt	Create an empty file
cp topol.top backup/	Copy a file
mv old.gro new.gro	Rename or move a file
rm file.log	Delete a file (no undo - be careful)
rm -r old_run/	Delete a directory and its contents

Viewing files

Command	What it does
cat file.mdp	Print an entire file to the screen
less file.log	Scroll through a large file (q to quit)
head -n 20 file.log	Show the first 20 lines
tail -n 20 file.log	Show the last 20 lines
tail -f md.log	Watch a file update live as a run writes to it

Searching

Command	What it does
grep "error" md.log	Find lines containing "error"
grep -i "warning" md.log	Same, but case-insensitive
grep -r "TODO" .	Search recursively through every file in a folder

Permissions and processes

Command	What it does
chmod +x script.sh	Make a script executable
top	Live view of running processes and CPU/memory use
ps aux	List all running processes
kill 12345	Stop a process by its ID

Redirection and pipes

Symbol	What it does
command > file.txt	Write output to a file (overwrite)
command >> file.txt	Append output to a file
command1 | command2	Send the output of one command into another

Example: gmx mdrun -deffnm em > run.log 2>&1 runs a simulation and saves all its output (including errors) to run.log.

Archives

Command	What it does
tar -czvf archive.tar.gz folder/	Compress a folder into a .tar.gz archive
tar -xzvf archive.tar.gz	Extract a .tar.gz archive

A note on case-sensitivity

Linux paths are case-sensitive. Topol.top and topol.top are two different files - a very common source of confusing "file not found" errors when following along with a tutorial.