Selecting workflows

Official Amber:

• https://ambermd.org/tutorials/

• JW – From here, I might suggest:

  • 1.3 Building Systems with CHARMM-GUI

    • Preparation of protein/N-glycan/ligand/membrane complex (5O8F)

    • Preparation of protein/DNA/RNA complex (6O0Z)

  • 1.8 Un-natural amino acids: the Amber ff15ipq-m force field

  • 1.10 Using the Pantetheine Force Field Library

  • 1.11 Building and Simulating an Ionic Liquid

  • a. Protein-Metal

  • b. PET polymer

  • c. Hydroxyapatite-Water

  • 2.1 Simulating a pharmaceutical compound with Antechamber and GAFF

  • 2.2 Setting up a DNA-Ligand System
    2.3 Simulating the Green Fluorescent Protein and building a modified amino acid residue

  • 2.4 Metal Ion Modeling Tutorial

  • 3.2 Relaxation of Implicit Solvent System (GB)

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:

• https://openmm.github.io/openmm-cookbook/latest/notebooks/tutorials/Histone_methyltransferase_simulation_with_a_multisite_water_model_TIP4P-Ew.html Some protein with TIP3P/TIP4P-EW/TIP5P:

• https://openmm.github.io/openmm-cookbook/latest/notebooks/tutorials/protein_in_water.html Basic protein PDB to simulation in water

• https://openmm.github.io/openmm-cookbook/latest/notebooks/tutorials/HSP90_with_ADPMg2_simulation.html Protein, Amber force field, and crazy Mg2+ interaction

• https://openmm.github.io/openmm-cookbook/latest/notebooks/cookbook/first_simulation.html Maybe re-do with Sage?

Lemkul:

• http://www.mdtutorials.com/gmx/lysozyme/index.html Lysozyme in water

• http://www.mdtutorials.com/gmx/membrane_protein/index.html Membrane protein

• http://www.mdtutorials.com/gmx/umbrella/index.html Umbrella sampling

  • JW – What from this tutorial would we want to match/compare to? I recommend deleting

• http://www.mdtutorials.com/gmx/biphasic/index.html Biphasic system

• http://www.mdtutorials.com/gmx/complex/index.html Protein-ligand complex

• http://www.mdtutorials.com/gmx/free_energy/index.html SFE via WHAM

• http://www.mdtutorials.com/gmx/vsites/index.html CO2 with virtual sites

Gravelle:

• https://gromacstutorials.github.io/

  • https://gromacstutorials.github.io/doc-sphinx/build/html/tutorials/bulksolution.html Not sure how well the ions might work

• https://lammpstutorials.github.io/

  • https://lammpstutorials.github.io/sphinx/build/html/tutorials/level1/lennard-jones-fluid.html Doubt our infrastructure handles non-elemental atoms well

  • https://lammpstutorials.github.io/sphinx/build/html/tutorials/level1/breaking-a-carbon-nanotube.html Looks to mostly be fancy LAMMPS-only stuff, not much system prep involved

  • https://lammpstutorials.github.io/sphinx/build/html/tutorials/level3/water-adsorption-in-silica.html Maybe doable

• NMR? https://nmrformd.readthedocs.io/en/latest/#

  • JW – It’s not clear what would uniquely be added by this, but maybe I’m overlooking something. Not easy to extract gro and top files → I recommend removing

Utah:

• https://amberhub.chpc.utah.edu/tutorials/ These seem to be mostly focused on post-processing and/or use GUIs

  • JW – Would recommend removing

mkvistes

• Exotic and not updated in years

  • JW – Would recommend removing