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Unwrapping NPT simulations to calculate diffusion coefficients
Jakob Tómas Bullerjahn, Sören von Bülow, Maziar Heidari +2
In molecular dynamics simulations in the NPT ensemble at constant pressure, the size and shape of the periodic simulation box fluctuate with time. For particle images far from the…
Systematic errors in diffusion coefficients from long-time molecular dynamics simulations at constant pressure
Sören von Bülow, Jakob Tómas Bullerjahn, Gerhard Hummer
In molecular dynamics simulations under periodic boundary conditions, particle positions are typically wrapped into a reference box. For diffusion coefficient calculations using th…
Optimal estimates of diffusion coefficients from molecular dynamics simulations
Jakob Tómas Bullerjahn, Sören von Bülow, Gerhard Hummer
Translational diffusion coefficients are routinely estimated from molecular dynamics simulations. Linear fits to mean squared displacement (MSD) curves have become the de facto sta…