Molecular modeling and simulation are important tools in biological sciences, as they provide insight into structures, dynamics, and underlying mechanisms of such systems, which are difficult to obtain from experimental data alone. In the past decade, the number of scientists using molecular simulations has expanded enormously, beyond the community of computational physicists and chemists that developed algorithms and force fields. An issue that is not always fully appreciated is the difficulty to prepare and initiate the complex computational tasks needed to achieve a specific objective. For example, setting up biomolecular simulations remains a complicated task, particularly when systems involve lipids, carbohydrates, modified proteins, complex solvents, etc. The choice of the most efficient software also depends on the platform and specificity of the system studied.
CHARMM-GUI is a web-based graphical user interface (GUI) to interactively setup complex biomolecular systems and input files for simulations using CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, and OpenMM programs. CHARMM-GUI now contains a number of different modules designed to setup a broad range of simulations to carry out innovative and novel biomolecular modeling and simulation research. In addition, the development of online lecture series on molecular modeling and simulation is ongoing in CHARMM-GUI Lectures. We will use these modules for lectures and tutorials in this School.
1. 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).
2. Glycan Reader for preparation of simulation systems containing carbohydrates or glycoproteins.
3. Ligand Reader & Modeler for generation of force field (FF) for ligands.
4. Glycolipid and LPS Modeler for generation of various glycolipid and lipopolysaccharide structures, respectively.
5. Quick MD Simulator for solution simulation system generation.
6. Membrane Builder for generation of bilayer, monolayer, micelle, nanodisc, hexagonal lipid phase, and vesicle systems with and without proteins.
7. Crowding System Builder in solution and membrane environments
8. HMMM Builder for building membrane systems using the highly mobile membrane mimetic (HMMM) model
9. PACE CG Builder and Martini Maker for coarse-grained simulations using the PACE FF and the Martini FF, respectively.
10. PBEQ-Solver for electrostatic potential online visualization.
11. GCMC/BD ion simulator for Brownian dynamics of ions across ion channels.
12. 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
13. DEER Spin-Pair Distributor to calculate the spin-pair distance distribution and reMD Prepper to setup a restrained-ensemble MD (reMD) simulation based on double electron-electron resonance (DEER) data
14. Drude Prepper for conversion of CHARMM additive FF-based systems to Drude polarizable FF-based systems.
15. Ligand Binder for free energy perturbation MD simulations for protein-ligand binding affinity calculations.
16. Presentations from participants