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Although molecular dynamics methods are commonly used to drive biomolecular simulations, the technique provides insufficient sampling to impact studies of the 200-300 residue proteins of greatest interest. One severe limitation of molecular dynamics is that the integrators are restricted by resonance phenomena to small time steps (Delta t<8 fs) much slower then the time scales of important structural and solvent rearrangements. Here, a novel set of equations of motion and a reversible, resonance-free, integrator are designed which permit step sizes on the order of 100 fs to be used.

Original publication

DOI

10.1103/PhysRevLett.93.150201

Type

Journal article

Journal

Phys Rev Lett

Publication Date

08/10/2004

Volume

93

Keywords

Algorithms, Biopolymers, Computer Simulation, HIV Protease, Models, Chemical, Molecular Conformation, Static Electricity, Thermodynamics, Water