title: Long time molecular dynamics for enhanced conformational sampling in biomolecular systems.
abstract: 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.
authors.affiliation: Department of Chemistry, New York University, New York, New York 10003, USA.
authors.forename: P
authors.initials: P
authors.lastname: Minary
authors.forename: M E
authors.initials: ME
authors.lastname: Tuckerman
authors.forename: G J
authors.initials: GJ
authors.lastname: Martyna
mesh_terms: D000465:Algorithms; D001704:Biopolymers / Q000737:chemistry*; D003198:Computer Simulation; D016333:HIV Protease / Q000737:chemistry; D008956:Models, Chemical; D008968:Molecular Conformation; D055672:Static Electricity; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D001704:Biopolymers; D014867:Water; D016333:HIV Protease