Long time molecular dynamics for enhanced conformational sampling in biomolecular systems

Phys Rev Lett. 2004 Oct 8;93(15):150201. doi: 10.1103/PhysRevLett.93.150201. Epub 2004 Oct 8.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Biopolymers / chemistry*
  • Computer Simulation
  • HIV Protease / chemistry
  • Models, Chemical*
  • Molecular Conformation
  • Static Electricity
  • Thermodynamics
  • Water / chemistry

Substances

  • Biopolymers
  • Water
  • HIV Protease