On the application of accelerated molecular dynamics to liquid water simulations.
Our group recently proposed a robust bias potential function that can be used in an efficient all-atom accelerated molecular dynamics (MD) approach to simulate the transition of high energy barriers without any advance knowledge of the potential-energy landscape. The main idea is to modify the potential-energy surface by adding a bias, or boost, potential in regions close to the local minima, such that all transitions rates are increased. By applying the accelerated MD simulation method to liquid water, we observed that this new simulation technique accelerates the molecular motion without losing its microscopic structure and equilibrium properties. Our results showed that the application of a small boost energy on the potential-energy surface significantly reduces the statistical inefficiency of the simulation while keeping all the other calculated properties unchanged. On the other hand, although aggressive acceleration of the dynamics simulation increases the self-diffusion coefficient of water molecules greatly and dramatically reduces the correlation time of the simulation, configurations representative of the true structure of liquid water are poorly sampled. Our results also showed the strength and robustness of this simulation technique, which confirm this approach as a very useful and promising tool to extend the time scale of the all-atom simulations of biological system with explicit solvent models. However, we should keep in mind that there is a compromise between the strength of the boost applied in the simulation and the reproduction of the ensemble average properties.
de Oliveira
César Augusto F
CA
Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA. cesar@mccammon.ucsd.edu
Hamelberg
Donald
D
McCammon
J Andrew
JA
D000465:Algorithms; D019295:Computational Biology; D003198:Computer Simulation; D004058:Diffusion; D004735:Energy Transfer; D008968:Molecular Conformation; D010100:Oxygen / Q000737:chemistry; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D013997:Time Factors; D014867:Water / Q000737:chemistry*
D012997:Solvents; D014867:Water; D010100:Oxygen