Journal of Molecular Graphics 

TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.

TL;DR: Special efforts were made to allow for appropriate display and analysis of the sets of typically 20-40 conformers that are conventionally used to represent the result of an NMR structure determination, using functions for superimposing sets of conformers, calculation of root mean square distance (RMSD) values, identification of hydrogen bonds, and identification and listing of short distances between pairs of hydrogen atoms.

TL;DR: The menu-driven operation of WHAT IF, combined with the use of default values wherever user input is required, makes it very easy to use for a novice user while keeping full flexibility for more sophisticated studies.

TL;DR: DL_POLY_2.0 is a general-purpose parallel molecular dynamics simulation package developed at Daresbury Laboratory and designed to run on a wide range of computers: from single processor workstations to parallel supercomputers.

TL;DR: A method (HOLE) that allows the analysis of the dimensions of the pore running through a structural model of an ion channel is presented and can be used to predict the conductance of channels using a simple empirically corrected ohmic model.