Below are software tools meant to support research by making biomolecular tasks easier, directing researchers to existing software resources, or providing convenient molecular representations. The programs include the MD Service Suite, the Structural Biology Software Database, and the Java Molecular Viewer. All programs in this collection are provided for the benefit of the research community; support for the programs listed will vary.


LiquidLib is a comprehensive toolbox for analyzing classical and ab initio molecular dynamics simulations of liquids and liquid-like matter with applications to neutron scattering experiments

PHI: Parallel Hierarchy Integrator

PHI (Parallel Hierarchy Equations of Motion Integrator) is a software package for integrating the hierarchy equation of motion to compute the noise- averaged density matrix evolution for a quantum system in contact with a thermal environment. PHI is a multi-threaded program to run on shared memory computers.

MD Service Suite

The MDTools suite is a collection of programs, scripts, and utilities for researchers to make various modeling and simulation tasks easier, and to provide basic code and utilities which can be built up into larger toolsets.

Structural Biology Software Database

The Structural Biology Software Database contains programs which are thought to be of interest to researchers in the fields of structural biology, quantum chemistry, and bioinformatics.

Java Molecular Viewer

The Java Molecular Viewer (JMV) is a molecular viewer written in Java and Java3D. JMV is designed to be an easy-to-use platform neutral molecular visualization tool, which can be used standalone or integrated into other programs.


  • 06/20/2008 - Page created.