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Helicase

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made with VMD

The eagerly awaited 2.7 release of NAMD includes GPU acceleration, downloadable binaries for Linux clusters with InfiniBand networks, grid-based forces and extra bond/angle/torsion conformational restraints for molecular dynamics flexible fitting (MDFF), and a major enhancement of both alchemical and conformational free energy methods. Alchemical calculations gradually alter the chemical structure of a molecule during a simulation, monitoring the consequences of creating and deleting atoms via either free energy perturbation or thermodynamic integration. A soft-core correction may be employed to circumvent singularities when atoms are created. Conformational calculations can probe structural rearrangements along an arbitrary number of collective variables, including distances between atoms or groups of atoms, distances projected along an axis or in a plane, angles, torsions, eigenvectors, gyration radii, coordination, root mean-square displacements, orientations, and alpha-helicity. New variables can be introduced without recompilation. Free energy surfaces or potentials of mean force can be constructed using metadynamics, the adaptive biasing force method, umbrella sampling, and steered molecular dynamics. The collective variables capability of NAMD has allowed the simulation of the illustrated hexameric helicase. In the simulation, a single strand of DNA passes through the central core while the hexamer translocates or "walks" along the DNA, a mechanical process driven by the energy of ATP hydrolysis.