International Scholarly Research Notices / 2013 / Article / Fig 1

Research Article

Saving Significant Amount of Time in MD Simulations by Using an Implicit Solvent Model and Elevated Temperatures

Figure 1

Simulations with different box sizes. Three typical simulations with different box sizes (dimensions are set to the diameter of the system (largest distance between atoms) plus twice the specified distance of 1 nm, 3 nm, or 6 nm) for one NaCl molecule with explicit water in 450°K. The distance (nm) between the Na+ and the Cl ions is measured over time (ps). In the simulation of the 1 nm box (red) the distance returned to the baseline value (~0.26 nm) very quickly after the ions were separated. This artificial behavior does not happen with the 6 nm box (purple); however the simulation is much slower. This artifact occurs when using the 3 nm box (blue), but only after about 1000 ps, a time period long enough for our purposes.

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