Model Building and Visualization Software

The first step of atomistic modelling usually involves building and/or visualising a system. For this there is a variety of software available, some examples of which are given below.

Model Building

  • Materials Studio This is proprietary software requiring access to a (paid) licence. It has many capabilities and is especially useful for building multi-component, periodic systems such as adsorbates on a mineral surface.
  • Chem3D This is also proprietary software and ‘..enables synthetic chemists and biologists to generate 3D models of small molecules and biochemical compounds..’
  • VMD Visual Molecular Dynamics software is free and useful for ‘..displaying, animating and analyzing…’
  • AtomEye This atomistic configuration viewer is free
  • VESTA Visualization for Electronic and STructural Analysis -it’s free and ‘..s a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies.’
  • ATEN: DL_POLY compatible molecular graphics viewer and editor, written by Tristan Youngs
  • A comprehensive list linking to Wikipedia
  • Ionic Liquids FF DL_POLY I/O setup utility using Canongia-Lopes & Pádua FF, a de-facto, standard FF for many ionic liquids
  • Software to assist with molecular dynamics simulations (by C. Bernardes)

Visualization and Analysis

A few examples include:

  • Materials Studio
  • VMD ‘VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.’
  • VESTA ‘3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies.’
  • OVITO This is free and is a ‘.. scientific visualization and analysis software for atomistic and particle simulation data.’
  • XCrySDen This is a ‘..crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.’
  • dlputils ‘..collection of small utilities that will calculate various properties from molecular dynamics trajectories, as well as allow for some manipulation of those trajectories’
  • Travis Software General-purpose trajectory visualiser, that works with DL_POLY HISTORY files Reference paper
  • Paraview This is ‘an open-source, multi-platform data analysis and visualization application’ ideal for visualising and analysing data-based datasets, including Lattice Boltzmann Equation (LBE) trajectories from DL_MESO_LBE and some analysis results (e.g. localised properties, density maps) from DL_MESO_DPD.