Bioinformatics Molecular Dynamics

CHARMM

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CHARMM is the full form of Chemistry at HARvard Macromolecular Mechanics that is the molecular simulation program with wide application to many particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques including QM/MM, MM/CG, and a range of implicit solvent models. It is actively maintained by a large group of developers led by Martin Karplus.

Features

  • It firstly targets biological systems including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments. 
  • It also finds broad applications for inorganic materials with applications in materials design.
  • It has a comprehensive set of analysis and model building tools.
  • It achieves high performance on a variety of platforms including parallel clusters and GPUs and can be obtained here.

CHARMM is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program gives us a large suite of computational tools that include certain conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. In addition, the CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to certain platforms in both serial and parallel architectures. 

CHARMM’s input files can take the form of mini-programs written in the interpretive language of CHARMM commands, common tasks can be coded in a general way at the script level. It is also possible to use complex methods and simulation protocols at the level of the input file without changing the source code.

The CHARMM program allows for generating and analyzing a wide range of molecular simulations. The most basic kinds of simulation are minimizing a given structure and production runs of a molecular dynamics trajectory.

More advanced features include free energy perturbation (FEP), quasi-harmonic entropy estimation, correlation analysis and combined quantum, and quantum mechanics molecular mechanics (QM/MM) methods.

CHARMM is one of the oldest programs for molecular dynamics. It has accumulated many features, some of which are duplicated under several keywords with slight variants. This is an inevitable result of the many outlooks and groups working on CHARMM worldwide. The file for change-log, and CHARMM’s source code, are good places to look for the names and affiliations of the main developers. 

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