Day 1 (September 23)

< Morning Lecture: 9:00 - 12:00>

• 9:00 - 9:50 Molecular mechanics & force field (Jeff  Kladua)

• 10:00 - 10:50 Minimization & molecular dynamics (Jeff Kladua)

• 11:00 - 11:50 CHARMM-GUI Lectures & common errors (Jumin Lee / Wonpil Im)

• 12:00 - 13:00 Lunch

< Afternoon Practice>

• Introduction of participants (1-2 slides) 

• PDB Reader & Manipulator for reading PDB and PDBx/mmCIF structure files and modifying side chains (e.g., mutation, phosphorylation, protonation, heme coordination, lipid-tail linkers, GPI-linker, glycosylation, spin labels, fluorophores, and unnatural amino acids) 

• Glycan Reader & Modeler for preparation of simulation systems containing carbohydrates or glycoproteins

• Ligand Reader & Modeler for generation of force field (FF) for ligands

• Glycolipid and LPS Modeler for generation of various glycolipid and lipopolysaccharide structures 

• Nanomaterial Modeler and Polymer Builder for generation of various nanomaterials and polymer systems

• 17:00 -  Banquet

Day 2 (September 24)  

< Morning Lecture: 9:00 - 12:00>

• 9:00 - 9:50 Lipid membrane simulations (Jeff Kladua)

• 10:00 - 10:50 Martini force field (Siewert-Jan)

• 11:00 - 11:50 HMMM, PACE force field, MDFF/xMDFF (Yifei Qi)

• 12:00 - 13:00 Lunch

• 1:00 - 1:50 Enhanced sampling & free energy simulation (Yuji Sugita)

• < Afternoon Practice>

• • Solution Builder for solution simulation system generation. 

  • Membrane Builder for generation of bilayer, monolayer, micelle, nanodisc, hexagonal lipid phase, and vesicle systems with and without proteins

  • HMMM Builder for building membrane systems using the highly mobile membrane mimetic (HMMM) model

  • PACE CG Builder and Martini Maker for coarse-grained simulations using the PACE FF and the Martini FF

   

   

   

  Day 3 (September 25) 

   

  < Morning Lecture: 9:00 - 11:25>

  • 9:00 - 9:50 Advanced sampling techniques and free energy simulation (Bernie Brooks)

  • 10:00 - 10:25 Ligand Binder (Seonghoon Kim) 

  • 10:25 - 10:50 Multicomponent Assembler (Nathan Kern)

  • 11:00 - 11:25 Polymer Builder and Nanomaterial Modeler (Yeol Kyo Choi)

  • 11:30 - 11:55 Programing with CHARMM-GUI (Sunhwan Jo)

  • 12:00 - 13:00 Lunch

   

• < Afternoon Practice>

• Ligand Binder for free energy perturbation MD simulations for protein-ligand binding affinity calculations 
• Polymer Builder and Nanomaterial Modeler
• Multicomponent Assembler in solution and membrane
• PBEQ-Solver for electrostatic potential online visualization. 
• MDFF/xMDFF Utilizer for MDFF/xMDFF Utilizer for setting up molecular dynamics flexible fitting (MDFF) simulation system inputs using electron density maps and low resolution crystallographic data as restraints Presentations from participants