Gromacs Demo

Files accompanying Max's November 2022 gromacs crash course.

DNA Demo

1. Building the DNA

   • Open avogadro
   • Build > Insert > DNA/RNA
   • Click compass to navigate
   • File > SaveAs (dna_AVO.pdb)
   • Inspect in text editor

2. Preparing the PDB for Gromacs

   • launch python3 and go through prep.py
   • or just execture ./prep.py
   • Inspect result in text editor

3. Running pdb2gmx

   • login to EUREKA
   • (optionally) ssh into debug node
   • go through top_1.sh
   • or just execute as ./top_1.sh
   • inspect files

4. Solvating and neutralising the system

   • go through top_2.sh
   • or just execute as ./top_2.sh

5. Running minimisation

   • go through min.sh
   • or just execute as ./min.sh

6. Basic analysis

   • see graph created by min.sh

7. Visualisation

   • load trajectory in VMD
   • Graphics > Representations
   • Extensions > Analysis > RMSD Trajectory Tool

8. Python analysis

   • see dhb.py