Improving the speed of volumetric density map generation via cubic spline interpolation.
Visualizing data generated from molecular dynamics simulations can be difficult, particularly when there can be thousands to millions of trajectory frames. The creation of a 3D grid of atomic density (i.e. a volumetric map) is one way to easily view the long-time average behavior of a system. One way to generate volumetric maps is by approximating each atom with a Gaussian function centered on that atom and spread over neighboring grid cells. However the calculation of the Gaussian function requires evaluation of the exponential function, which is computationally costly. Here we report on speeding up the calculation of volumetric maps from molecular dynamics trajectory data by replacing the expensive exponential function evaluation with an approximation using interpolating cubic splines. We also discuss the errors involved in this approximation, and recommend settings for volumetric map creation based on this.
['Roe|Daniel R|DR|', 'Brooks|Bernard R|BR|']
D056004:Molecular Dynamics Simulation
Molecular dynamics Volumetric maps Grid density Trajectory analysis