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- W2794083527 abstract "Over the past 10 years, CHARMM-GUI (http://www.charmm-gui.org) has been developed to provide a user-friendly interface with various modules to read and manipulate PDB structure files (both in PDB and PDBx/mmCIF formats) and to build complex biomolecular systems reliably. It also provides various force field topology and parameter information for most commonly used molecules, so that users can almost always find what they need for their biomolecular systems. To support broader simulation communities, CHARMM-GUI now provides CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, and OpenMM inputs with well-validated, optimized protocols. To supplement the tools on CHARMM-GUI, we have designed a series of online tutorials (http://www.charmm-gui.org/lecture). These tutorials introduce useful tools and concepts in molecular modeling and simulation to high school and undergraduate college students. Furthermore, to aid in introducing students to UNIX, we have included a web interface to a virtual machine running the Ubuntu operating system. Topics include: the UNIX operating system, text editors, scientific programming using the Python programming language, PDB basics, molecule drawing, all-atom energy function & force fields, coarse-grained force fields, boundary conditions, ensembles, particle mesh Ewald methods, minimization, normal mode analysis, monte Carlo, dynamics (molecular dynamics, Langevin dynamics, and Brownian dynamics), introduction to complex systems (biological and other complex fluids), implicit solvents, replica exchange methods, alchemical free energy calculations, umbrella sampling free energy calculations, path sampling, QM/MM, introduction to protein structure prediction (homology modeling, sequence alignment, ab initio modeling), and introduction to protein-ligand docking (scoring function, sampling method, virtual screening). Many of these modules are under development, but most of the basic modules are already available." @default.
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- W2794083527 date "2018-02-01" @default.
- W2794083527 modified "2023-10-16" @default.
- W2794083527 title "CHARMM-GUI Lecture Series on Molecular Modeling and Simulation" @default.
- W2794083527 doi "https://doi.org/10.1016/j.bpj.2017.11.1027" @default.
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