Calculation of 1D and 2D densities in VMD: A flexible and easy-to-use code

Visualization of the density distribution is typically one of the most important properties in structural characterization. Visual Molecular Dynamics (VMD) is a widely used molecular visualization package that can not only visualize complex molecular systems but also perform analysis by integrating special plugins or by running in-house generated TCL scripts.

However, a density analysis is still not an in-built feature of VMD. This work presents a flexible and easy-to-use TCL code to be used in VMD, that can perform both 1D and 2D density calculations over any specified local areas of a given system. By using the built-in commands of VMD, the code can access and process trajectory files in any formats that are supported by VMD, as produced by mainstream simulation packages, i.e., LAMMPS, GROMACS, NAMD, and CHARMM, etc.