Appendix

This chapter provides a brief overview of using the BioExcel Building Block (biobb) to prepare biomolecular systems for molecular dynamics simulations with GROMACS, starting from PDB file manipulation.

13 Introduction

Basic Linux Commands Useful for HPC: These commands are essential for navigating directories, managing files, and monitoring jobs on an HPC system.

File and Directory Management

• pwd — show current directory
• ls — list files
• ls -l — detailed file listing
• cd directory_name — change directory
• cd .. — move up one directory
• mkdir folder_name — create a directory
• rm file — delete a file
• rm -r folder — delete a directory (use carefully)

Viewing and Editing Files

• cat filename — display file contents
• less filename — view large files safely
• head filename — show first 10 lines
• tail filename — show last 10 lines
• nano filename — edit file (beginner-friendly)
• vi filename or vim filename — advanced editor commonly used on HPC

System and Job Monitoring

• whoami — show your username
• hostname — show compute/login node name
• top or htop — monitor running processes
• df -h — check disk usage
• du -sh folder_name — size of a directory

Job Scheduler (examples — cluster dependent) Actual commands depend on the scheduler used on BigDawg, such as SLURM

• sbatch job.sh — submit a job
• squeue -u username — check job status
• scancel jobID — cancel a job