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| CHARMM36 | |
|---|---|
| Name | CHARMM36 |
| Developer | Johns Hopkins University; University of California, San Diego; Harvard University; Columbia University research groups; University of Groningen contributors |
| Released | 2010s |
| Latest release | ongoing updates |
| Programming language | Fortran; C; C++ |
| Operating system | Linux; Windows NT; macOS |
| License | academic; commercial integrations |
CHARMM36 CHARMM36 is a widely used additive biomolecular force field for molecular dynamics that builds on the CHARMM family of potentials and parameter sets. It provides parametrizations for proteins, lipids, nucleic acids, carbohydrates, and small molecules and is used across computational studies in institutions such as Stanford University, Massachusetts Institute of Technology, Princeton University, Yale University, and University of Chicago. The force field underpins simulations performed with software developed at projects including CHARMM, NAMD, GROMACS, AMBER, and LAMMPS.
CHARMM36 is an additive potential energy model originally developed within the MacKerell lab context at University of Maryland, Baltimore County and further advanced by collaborative groups at D. E. Shaw Research, University of Pennsylvania, University of California, San Diego, and National Institutes of Health. It refines intermolecular interactions used in classical molecular dynamics to reproduce experimental observables from techniques performed at facilities such as Brookhaven National Laboratory and Argonne National Laboratory. CHARMM36 is commonly compared with alternative parameter sets from AMBER ff14SB, OPLS-AA, GROMOS, and polarizable models like AMOEBA.
Development of CHARMM36 followed iterative fitting protocols employed by researchers affiliated with National Institute of Standards and Technology collaborations and with benchmarks against quantum chemistry methods from groups at California Institute of Technology and Massachusetts Institute of Technology. Parametrization steps referenced data from quantum calculations performed with codes developed at Gaussian, Inc. and teams using Psi4 and Q-Chem packages, and experimental constraints from structural biology centers including European Molecular Biology Laboratory, Max Planck Institute for Biophysical Chemistry, and EMBL-EBI. The process involved comparisons to thermodynamic quantities measured by laboratories such as Columbia University Irving Medical Center and spectroscopy data from laboratories at University of Cambridge and ETH Zurich.
The functional form in CHARMM36 retains the classical bonded and nonbonded terms used in earlier parameter sets developed at Merck Research Laboratories and within the original CHARMM consortium. Bonded terms include bond stretching, angle bending, and dihedral torsions calibrated against ab initio potentials from groups at Princeton University and Yale University. Nonbonded interactions use Lennard-Jones potentials and Coulombic terms with partial charges derived by protocols influenced by methods from Harvard University and Cornell University. Water models compatible with CHARMM36, such as those influenced by developments at University of Illinois Urbana-Champaign and University of Southampton, are tuned to reproduce properties measured at National Renewable Energy Laboratory and other experimental centers.
Validation studies for CHARMM36 were performed by collaborative teams at University of California, Berkeley, University of Michigan, University of Texas at Austin, and University of Washington, benchmarking against NMR, X-ray crystallography, and calorimetry data reported by groups at Scripps Research Institute and Cold Spring Harbor Laboratory. Performance comparisons often involve test systems studied at Lawrence Berkeley National Laboratory and include lipid bilayer properties measured at NIH. CHARMM36 is recognized for improved reproduction of lipid order parameters relative to earlier CHARMM versions, matching experiments from laboratories such as Brandeis University and University of Oslo.
CHARMM36 has been applied in studies of membrane proteins investigated by researchers at Rockefeller University and University of Texas Southwestern Medical Center, nucleic acid conformational studies pursued at MRC Laboratory of Molecular Biology and Wellcome Trust Sanger Institute, carbohydrate dynamics examined by teams at University of Georgia and University of Strathclyde, and drug-binding simulations performed in collaborations with Pfizer and Novartis research groups. It is used in multiscale workflows connecting to coarse-grained models developed at Max Planck Institute for Polymer Research and in integrative modeling efforts incorporating data from European Synchrotron Radiation Facility and Diamond Light Source.
Limitations noted by researchers at Rutgers University and Ohio State University include challenges reproducing polarization effects emphasized by groups at IBM Research and handling extreme pH or redox states studied at Lawrence Livermore National Laboratory. Extensions and improvements have been proposed by teams at University of California, San Francisco and University of Pennsylvania, including Drude polarizable models and CMAP corrections that draw on methodologies from University of Minnesota and Duke University. Comparative assessments against machine-learned potentials explored by groups at Google DeepMind and Facebook AI Research highlight ongoing avenues for enhancement.
CHARMM36 parameters are distributed with the CHARMM program maintained by the original consortium and are implemented in production molecular dynamics engines including NAMD, GROMACS, AMBER (via conversion), and LAMMPS. These implementations are supported by community contributions from repositories hosted by GitHub collaborators at academic groups such as University of Pennsylvania and University of California, San Diego, and are incorporated into workflows run on high-performance systems at Oak Ridge National Laboratory and National Energy Research Scientific Computing Center. Training materials and tutorials leveraging CHARMM36 have been offered by European Molecular Biology Laboratory courses and workshops at Cold Spring Harbor Laboratory.
Category:Force fields