Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS.
Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.
Grindon
Christina
C
School of Pharmaceutical Sciences, University of Nottingham, Nottingham NG7 2RD, UK.
Harris
Sarah
S
Evans
Tom
T
Novik
Keir
K
Coveney
Peter
P
Laughton
Charles
C
D000465:Algorithms; D001483:Base Sequence; D003198:Computer Simulation; D003205:Computing Methodologies; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D004548:Elasticity; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009038:Motion; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D013314:Stress, Mechanical
D004247:DNA