Paper Citing NAMD - Abstract
Savelyev, Alexey; MacKerell, Alexander D., Jr.
Competition among Li+, Na+, K+, and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields
JOURNAL OF PHYSICAL CHEMISTRY B, 119:4428-4440, MAR 26 2015
In the present study we report on interactions of and competition between monovalent ions for two DNA sequences in MD simulations. Efforts included the development and validation of parameters for interactions among the first-group monovalent cations, Li+, Na+, K+, and Rb+, and DNA in the Drude polarizable and additive CHARMM36 force fields (FF). The optimization process targeted gas-phase QM interaction energies of various model compounds with ions and Osmotic pressures of bulk electrolyte solutions of chemically relevant ions. The optimized ionic parameters are validated against counterion condensation theory and buffer exchange-atomic emission spectroscopy measurements providing quantitative data on the competitive association of different monovalent ions with DNA. Comparison between experimental and MD simulation results demonstrates that, compared to the additive CHARMM36 model, the Drude FF provides an improved description of the general features of the ionic atmosphere around DNA and leads to closer agreement with experiment on the ionic competition within the ion atmosphere. Results indicate the importance of extended simulation systems on the order of 25 angstrom beyond the DNA surface to obtain proper convergence of ion distributions.
