Selecting workflows

Official Amber:

• https://ambermd.org/tutorials/

Official GROMACS:

• https://tutorials.gromacs.org/membrane-protein.html uses CHARMM-GUI

• https://tutorials.gromacs.org/free-energy-of-solvation.html SFE via AWH

Official OpenMM cookbook:

• Some protein with TIP3P/TIP4P-EW/TIP5P:

• Basic protein PDB to simulation in water

• Protein, Amber force field, and crazy Mg2+ interaction

• Maybe re-do with Sage?

Lemkul:

• Lysozyme in water

• Membrane protein

• Umbrella sampling

• Biphasic system

• Protein-ligand complex

• SFE via WHAM

• CO2 with virtual sites

Gravelle:

• • Not sure how well the ions might work

• • Doubt our infrastructure handles non-elemental atoms well

  • Looks to mostly be fancy LAMMPS-only stuff, not much system prep involved

  • Maybe doable

• NMR?

Utah:

• These seem to be mostly focused on post-processing and/or use GUIs

mkvistes

• Exotic and not updated in years