Efficient molecular dynamics using geodesic integration and solvent–solute splitting

We present an approach to Langevin dynamics in the presence of holonomic constraints based on decomposition of the system into components representing geodesic flow, constrained impulse and constrained diffusion. We show that a particular ordering of the components results in an integrator that is a...

Full description

Saved in:
Bibliographic Details
Published inProceedings of the Royal Society. A, Mathematical, physical, and engineering sciences Vol. 472; no. 2189; pp. 1 - 22
Main Authors Leimkuhler, Benedict, Matthews, Charles
Format Journal Article
LanguageEnglish
Published THE ROYAL SOCIETY 01.05.2016
Subjects
Atoms
Dynamic efficiency
Mathematical vectors
Molecular dynamics
Molecules
Potential energy
Proteins
Simulations
Solutes
Solvents
Online AccessGet full text

Cover

More Information
Summary:We present an approach to Langevin dynamics in the presence of holonomic constraints based on decomposition of the system into components representing geodesic flow, constrained impulse and constrained diffusion. We show that a particular ordering of the components results in an integrator that is an order of magnitude more accurate for configurational averages than existing alternatives. Moreover, by combining the geodesic integration method with a solvent–solute force splitting, we demonstrate that stepsizes of at least 8fs can be used for solvated biomolecules with high sampling accuracy and without substantially altering diffusion rates, approximately increasing by a factor of two the efficiency of molecular dynamics sampling for such systems. The methods described in this article are easily implemented using the standard apparatus of modern simulation codes.
ISSN:1364-5021
1471-2946