Paper Citing NAMD - Abstract
Liu, Yufeng; Haddadian, Esmael; Sosnick, Tobin R.; Freed, Karl F.; Gong, Haipeng
A Novel Implicit Solvent Model for Simulating the Molecular Dynamics of RNA
BIOPHYSICAL JOURNAL, 105:1248-1257, SEP 3 2013
Although molecular dynamics simulations can be accelerated by more than an order of magnitude by implicitly describing the influence of the solvent with a continuum model, most currently available implicit solvent simulations cannot robustly simulate the structure and dynamics of nucleic acids. The difficulties become exacerbated especially for RNAs, suggesting the presence of serious physical flaws in the prior continuum models for the influence of the solvent and counter ions on the nucleic acids. We present a novel, to our knowledge, implicit solvent model for simulating nucleic acids by combining the Langevin-Debye model and the Poisson-Boltzmann equation to provide a better estimate of the electrostatic screening of both the water and counter ions. Tests of the model involve comparisons of implicit and explicit solvent simulations for three RNA targets with 20, 29, and 75 nucleotides. The model provides reasonable agreement with explicit solvent simulations, and directions for future improvement are noted.
