Gromacs Demo
Files accompanying Max's November 2022 gromacs crash course.
DNA Demo
-
Building the DNA
- Open avogadro
- Build > Insert > DNA/RNA
- Click compass to navigate
- File > SaveAs (dna_AVO.pdb)
- Inspect in text editor
-
Preparing the PDB for Gromacs
- launch python3 and go through prep.py
- or just execture ./prep.py
- Inspect result in text editor
-
Running pdb2gmx
- login to EUREKA
- (optionally) ssh into debug node
- go through top_1.sh
- or just execute as ./top_1.sh
- inspect files
-
Solvating and neutralising the system
- go through top_2.sh
- or just execute as ./top_2.sh
-
Running minimisation
- go through min.sh
- or just execute as ./min.sh
-
Basic analysis
- see graph created by min.sh
-
Visualisation
- load trajectory in VMD
- Graphics > Representations
- Extensions > Analysis > RMSD Trajectory Tool
-
Python analysis
- see dhb.py