Long time molecular dynamics for enhanced conformational sampling in biomolecular systems.
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.
Minary
P
P
Department of Chemistry, New York University, New York, New York 10003, USA.
Tuckerman
M E
ME
Martyna
G J
GJ
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
D001704:Biopolymers; D014867:Water; D016333:HIV Protease