CHARMM-GUI

CHARMM-GUI generates all-atom models and simulation input files for molecular dynamics studies of complex biological membranes and membrane-associated systems.

Key Features:

• Membrane Builder: Constructs all-atom protein/membrane and membrane-only systems and supports over 180 lipid types including phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol, with procedures for optimized lipid packing and detection of lipid tail penetration into ring structures and protein surfaces.
• Glycolipid and LPS Modeler: Generates all-atom structures for glycoglycerolipids, glycosphingolipids, glycosylphosphatidylinositol, lipopolysaccharides (LPS), and lipooligosaccharides (LOS).
• Simulation Protocol Optimization: Produces optimized protocols and input files for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM with parameterization for the CHARMM36 (C36) force field and systematic testing of Lennard-Jones cutoff schemes and integrator algorithms for nonbonded interaction treatment.
• Advanced Algorithms: Implements distance-based algorithms for ion displacement and provides P21 image transformation and equilibration/production input generation for NAMD simulations.

Scientific Applications:

• Membrane structure and dynamics: Enables investigation of the structure, organization, and dynamic behavior of complex biological lipid bilayers.
• Glycolipid and lipoglycan studies: Supports modeling and simulation of glycolipids, lipoglycans, LPS, and LOS to study their structural roles in membranes.
• Membrane protein–lipid interactions: Facilitates all-atom simulations of membrane proteins and their interactions with diverse lipid environments.

Methodology:

Uses the CHARMM force field (including CHARMM36 for lipids), generates simulation input and equilibration/production files for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM, applies optimized protocols with systematic testing of Lennard-Jones cutoff schemes, integrator algorithms, and nonbonded interaction treatments, and supports analysis of atomic coordinates and simulation trajectories.