To build a spatial distribution function one should fix the local coordinate system. For large molecules it may be done in different ways. Picture to the right explains how we fix the local coordinate system using four phosphates of two neighbouring base pairs. On the pictures below we displayed the averaged structures of a two base pairs fragment and spatial distribution functions of ions around it. Li ions distribution around phosphate.
Installation is easy.
Normally one need only to download the file corresponding your platform, unpack it and run Install script. After completing the installation setup GOpenMol as a helper application for your Web browser. If your have installed GOpenMol but were not successful in setting up it as a helper application, you can download the files with spatial distribution functions onto your local disk and then open them with GOpenMol program. Simulation details The molecular dynamics simulations were performed using MDynaMix program. Simulation time 2 ns for Li and Na and 1 ns for Cs.