CHARMM : A program for macromolecular energy, minimization, and dynamics calculations¶
Why this mattered¶
TBD
Abstract¶
Abstract CHARMM ( C hemistry at HAR vard M acromolecular M echanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build structures, energy minimize them by first‐ or second‐derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.
Related¶
- cite → An algorithm for the machine calculation of complex Fourier series — CHARMM cites the fast Fourier transform algorithm for efficient calculation of periodic electrostatic and structural terms.
- cite → A general method applicable to the search for similarities in the amino acid sequence of two proteins — CHARMM cites Needleman-Wunsch sequence alignment as a method for identifying homologous protein segments before structural modeling.
- enables → Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems — CHARMM enables particle mesh Ewald by providing the molecular dynamics setting where efficient long-range electrostatic energy calculations are needed.
- enables → All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins — CHARMM provided the macromolecular simulation framework in which the 1998 all-atom empirical protein potential was implemented and validated.
- cite ← Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems — Particle mesh Ewald was developed for molecular dynamics force-field calculations of the kind implemented in CHARMM.
- cite ← All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins — The all-atom empirical potential was developed for use within the CHARMM macromolecular energy minimization and dynamics framework.
- enables ← An algorithm for the machine calculation of complex Fourier series — The FFT enabled CHARMM by making efficient spectral and long-range numerical calculations practical in molecular simulation workflows.
- enables ← A general method applicable to the search for similarities in the amino acid sequence of two proteins — Needleman-Wunsch sequence alignment enabled CHARMM by supporting comparative protein sequence analysis used alongside macromolecular modeling.