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CHARMM‐GUI,http://www.charmm-gui.org, is a web‐based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM‐GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Since its original development in 2006, CHARMM‐GUI has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of simulations: (1)PDB Reader & Manipulator,Glycan Reader, andLigand Reader & Modelerfor reading and modifying molecules; (2)Quick MD Simulator,Membrane Builder,Nanodisc Builder,HMMM Builder,Monolayer Builder,Micelle Builder, andHex Phase Builderfor building all‐atom simulation systems in various environments; (3)PACE CG BuilderandMartini Makerfor building coarse‐grained simulation systems; (4)DEER FacilitatorandMDFF/xMDFF Utilizerfor experimentally guided simulations; (5)Implicit Solvent Modeler,PBEQ‐Solver, andGCMC/BD Ion Simulatorfor implicit solvent related calculations; (6)Ligand Binderfor ligand solvation and binding free energy simulations; and (7)Drude Prepperfor preparation of simulations with the CHARMM Drude polarizable force field. Recently, new modules have been integrated into CHARMM‐GUI, such asGlycolipid Modelerfor generation of various glycolipid structures, andLPS Modelerfor generation of lipopolysaccharide structures from various Gram‐negative bacteria. These new features together with existing modules are expected to facilitate advanced molecular modeling and simulation thereby leading to an improved understanding of the structure and dynamics of complex biomolecular systems. Here, we briefly review these capabilities and discuss potential future directions in the CHARMM‐GUI development project. © 2016 Wiley Periodicals, Inc.