Some useful links
Structure, visualization, and analysis
Jmol is an open-source Java viewer for chemical structures in 3D.
VMD is a molecular visualization system for displaying and animating biomolecules, maintained by the Theoretical and Computational Biophysics Group at University of Illinois at Urbana-Champaign.
Avogadro is a free and open source molecule editor.
UCSF Chimera is a visualization and analysis software for biological molecules.
PyMOL is a molecular visualization system, maintained by Schrödinger
Molecular dynamics codes
GROMACS is a free and open source molecular dynamics package that can perform classical molecular mechanics.
LAMMPS is a classical molecular dynamics code with a focus on materials modeling. LAMMPS is distributed by Sandia National Laboratories, a US Department of Energy laboratory.
CP2K is a free and open source quantum chemistry and molecular dynamics package. It supports both quantum and classical molecular mechanics, and hybrid QM/MM simulations.
CPMD a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics
Topology generation and file format conversion
AmberTools is a part of Amber molecular dynamics package and is a freely available set of tools for preparation and analysis of molecular dynamics simulations.
Open Babel is free and open source software for converting between different chemical file formats.
Enhanced sampling
PLUMED2 is a free and open source library for enhanced sampling and free energy calculations in molecular systems.
Internal links
Lab wiki a set of tutorials hosted by our group on some of the methods we commonly use.