Research summary
The CHARMM (Chemistry at Harvard Macromolecular Mechanics) program for biomolecular simulation is described, providing structure reading and model building, energy minimization, normal-mode and molecular dynamics simulations, and analysis tools for macromolecular systems [1, 3]. An all-atom empirical potential for proteins was developed using a self-consistent procedure that balances internal (bonding) and interaction (nonbonding) terms and solvent-solute interactions, with backbone parameters tuned against N-methylacetamide and alanine dipeptide data and ab initio plus condensed-phase targets [2]. A combined QM/MM scheme using MNDO/AM1 semiempirical methods with the CHARMM force field was introduced to treat reactions in condensed phases, including prescriptions for QM/MM interactions across bond cuts and tests against ab initio and experimental data [5]. NMR spin-spin coupling theory was developed: a valence-bond treatment of contact electron-spin coupling reduced proton-proton, proton-fluorine, and fluorine-fluorine coupling-constant calculation in ethanic and ethylenic molecules to a tractable canonical-structures problem in good agreement with experiment [4], and vicinal proton coupling in NMR was analyzed in the well-known 1963 communication that underpins the Karplus equation [6]. Molecular dynamics was used for crystallographic R-factor refinement, incorporating the difference between observed and calculated structure factor amplitudes into the system energy and giving a larger radius of convergence than restrained least squares, demonstrated on crambin where misplaced residues moved more than 3 angstroms into correct positions without manual intervention [7]. Activation free energies in complex systems are formulated using the minimum-energy path with a local reaction coordinate that decomposes the free energy into segment-progression and direction-change contributions [8].
Recent publications
- CHARMM: A program for macromolecular energy, minimization, and dynamics calculationsDOI
- All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of ProteinsDOI
- CHARMM: The biomolecular simulation programDOI
- Molecular dynamics simulations of biomoleculesDOI
- Contact Electron-Spin Coupling of Nuclear Magnetic MomentsDOI
- A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulationsDOI
- Vicinal Proton Coupling in Nuclear Magnetic ResonanceDOI
- Dynamics of folded proteinsDOI
- Crystallographic R Factor Refinement by Molecular DynamicsDOI
- Simulation of activation free energies in molecular systemsDOI
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Email Martin Karplus 6-12 months before your application deadline. Read several recent papers and reference specific work in your message. Use our how to email a Japanese professor guide for the proven email structure.
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External profiles
- ORCID: https://orcid.org/0000-0002-5485-6117
- OpenAlex: openalex.org
Profile compiled from public sources (Researchmap, OpenAlex, The University of Tokyo faculty directory). Last refreshed 2026-05. Report incorrect information.