GENESIS

Tutorials

We show tutorials for basic and advanced MD simulations with GENESIS. These tutorials are useful for not only GENESIS beginners but also experts who want to know newly-introduced functions. Before starting the tutorials, the users are recommended to get VMD and gnuplot, both of which are free software, to visualize MD trajectories and plot data. GENESIS should be installed in your computer with OpenMPI. Note that in the tutorial we will use various linux commands such as grep, cut, paste, tail, sed, tee, and awk, and also utilize a pipe (|) to combine the commands. If you do not know their basic usage, learn them in advance.

1. Basic molecular dynamics simulations
   • 1.1 All-atom MD simulation of BPTI in NaCl solution
   • 1.2 All-atom MD simulation of POPC lipid bilayer
   • 1.3 Coarse-grained MD simulation with the Go model
2. Replica-exchange molecular dynamics simulations
   • 2.1 Temperature REMD simulations of a small peptide
   • 2.2 Replica-exchange umbrella sampling
   • 2.4 REST (Replica Exchange with Solute Tempering)
3. Advanced molecular dynamics simulations
   • 3.1 Large scale simulation using the parallel I/O
   • 3.2 String method
4. Trajectory analysis tools
   • 4.1 Root-mean-square deviation (RMSD)
   • 4.2 Distance, angle, dihedral angle
   • 4.3 Root-mean-square fluctuation (RMSF)
   • 4.4 Principal component analysis (PCA)

Appendix

• How to analyze multiple DCD files in the trajectory analysis tools?
• Automatic Parameter Tuning for REMD, REUS, REST