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| CHARMM force field | |
|---|---|
| Name | CHARMM force field |
| Developer | Martin Karplus, Axel Kohlmeyer, Berk Hess, Brooks Group |
| Initial release | 1983 |
| Latest release | ongoing |
| Programming languages | Fortran, C++, Python |
| License | mixed proprietary and open-source |
| Platform | Linux, Windows, macOS |
CHARMM force field The CHARMM force field is a widely used empirical potential set for molecular dynamics simulations developed to model biomolecules such as protein, nucleic acid, lipid, and carbohydrate systems. It was created within the CHARMM program development effort and has evolved through contributions from research groups associated with institutions like Harvard University, Harvard, Boston University, Columbia University, University of California, San Francisco, and National Institutes of Health. The force field informs simulations conducted with codes tied to computational chemistry, molecular modeling, and structural biology communities including AMBER (software), GROMACS, NAMD, LAMMPS, and Desmond.
The origins trace to the CHARMM program development in the early 1980s under the leadership of Martin Karplus and colleagues at Harvard University and collaborators at University of California, San Francisco and Boston University. Early parameter sets were influenced by experimental data from groups at National Institutes of Health and theoretical work by researchers at Bell Labs and Brookhaven National Laboratory. Subsequent milestones include integration of polarizable terms inspired by work at Pennsylvania State University and theoretical advances related to quantum chemistry performed at California Institute of Technology and Massachusetts Institute of Technology. Major community-driven updates involved collaborations with scientists at Princeton University, University of Cambridge, University of Oxford, Max Planck Society, and Riken. The CHARMM family’s dissemination intersected with developments in high-performance computing at Oak Ridge National Laboratory, Argonne National Laboratory, and supercomputing centers funded by National Science Foundation.
The functional form builds on bonded and nonbonded contributions formalized in early force field literature from groups at Harvard University and Brookhaven National Laboratory. Bonded terms include harmonic bond stretching, angle bending, and Fourier-series dihedral torsions with functional parallels to forms used by AMBER (software) and parameter philosophies from OPLS. Nonbonded interactions employ Lennard-Jones 12-6 potentials and Coulombic electrostatics, with long-range treatments leveraging Ewald summation methods developed at Princeton University and Rutgers University. Polarizable extensions adopt inducible dipole or Drude oscillator models influenced by theoretical chemical physics research at University of California, Berkeley and Stanford University. Constraint algorithms such as SHAKE and RATTLE, originating in work at IBM and Columbia University, are commonly used alongside multiple-time-step integrators from Max Planck Society collaborators.
Parameter derivation relied on quantum mechanical reference data computed using methods from Gaussian (software), DALTON (software), and research groups at University of Illinois Urbana–Champaign and University of Pittsburgh. Empirical fitting involved thermodynamic and spectroscopic benchmarks from experimental laboratories at National Institute of Standards and Technology, Brookhaven National Laboratory, and Lawrence Berkeley National Laboratory. Validation studies compared simulated ensemble properties to crystallographic coordinates in the Protein Data Bank and NMR datasets produced by investigators at Yale University and University of Michigan. Benchmarking efforts coordinated with software teams at The Scripps Research Institute and University of Texas Southwestern Medical Center ensured compatibility with community standards promoted by organizations such as American Chemical Society and Biophysical Society.
The CHARMM family expanded to specialized parameter sets for lipids, carbohydrates, and drug-like molecules with contributions from research groups at University of Illinois, University of Wisconsin–Madison, University of California, Santa Barbara, and University of Texas at Austin. Polarizable Drude oscillator variants were developed in collaborations involving Penn State University and University of North Carolina at Chapel Hill. Coarse-grained and multiscale mappings interfaced with methods from University of Groningen and ETH Zurich. Integration with enhanced sampling algorithms linked to groups at University of Chicago and Imperial College London allowed hybrid approaches combining CHARMM parameters with free-energy methods from University of California, San Diego.
CHARMM parameter sets underpin simulations of protein folding studies performed in labs at Stanford University and University of Cambridge, membrane biophysics research at Columbia University and Brandeis University, and ligand–receptor binding investigations by pharmaceutical teams at Pfizer, Novartis, and Merck & Co.. Structural refinement of macromolecular complexes used CHARMM-informed protocols in structural biology centers like European Molecular Biology Laboratory and Weizmann Institute of Science. Computational enzymology projects at Max Planck Institute for Biophysical Chemistry and Scripps Research employed CHARMM-based QM/MM schemes developed in collaboration with University of Minnesota and University of California, Irvine.
CHARMM parameters are implemented in major molecular simulation packages including CHARMM (program), NAMD, GROMACS, AMBER (software), LAMMPS, and proprietary platforms used by Schrödinger (company). Toolkits for parameter conversion and topology management were developed by teams at University of California, San Diego, University of Massachusetts Amherst, and Stanford University to facilitate interoperability with molecular visualization tools like VMD, PyMOL, and Chimera. High-throughput workflows running on infrastructure provided by Amazon Web Services, Microsoft Azure, and national supercomputing centers integrate CHARMM-based simulations into pipelines supported by funding from National Institutes of Health and National Science Foundation.
Critiques of CHARMM include challenges in transferability highlighted by researchers at University of Cambridge and Harvard University, and debates over empirical versus polarizable representations discussed in forums including meetings of Biophysical Society and publications involving Nature Methods and Journal of Chemical Theory and Computation. Performance trade-offs for polarizable variants prompted comparative studies at Argonne National Laboratory and Oak Ridge National Laboratory. Parameter coverage gaps for exotic chemistries were addressed in community efforts led by groups at University of California, Santa Cruz and Columbia University, while reproducibility concerns motivated open-data initiatives supported by PLOS and Science editorial policies.
Category:Force fields