Molecular Dynamics Simulation Engines

AMBER, CHARMM, GROMACS, and OpenMM are different molecular dynamics engines. They all can perform molecular dynamics simulations. One researcher does not need to learn all of them for performing molecular dynamics simulations. Just chose one to start!

1. The AMBER software package

a. The main webpage: https://ambermd.org/

b. Get AmberTools, which is free: https://ambermd.org/AmberTools.php

c. Get Amber: https://ambermd.org/AmberMD.php

d. AMBER tutorials: https://ambermd.org/tutorials/

e. AMBER manual: https://ambermd.org/Manuals.php

f. Dr. Jason Swails's wiki: http://jswails.wikidot.com/

2. The CHARMM software package:

a. The main webpage: https://www.charmm.org/

b. CHARMM tutorials: https://www.charmmtutorial.org/index.php/CHARMM_Tutorial

c. CHARMM documentation: https://www.charmm.org/charmm/documentation/

d. CHARMM-GUI: http://www.charmm-gui.org/

e. FFTK video tutorial: http://www.ks.uiuc.edu/Research/fftk/

3. The GROMACS software package:

a. The main webpage: http://www.gromacs.org/

b. GROMACS tutorials: http://www.gromacs.org/Documentation/Tutorials

c. GROMACS tutorials by Prof. Lemkul: http://www.mdtutorials.com/gmx/

d. GROMACS manual: http://manual.gromacs.org/documentation/

4. The OpenMM engine:

a. The main webpage: http://openmm.org/

b. OpenMMTools: https://openmmtools.readthedocs.io/en/0.18.1/index.html

c. OpenMM cookbook and tutorials: http://openmm.org/tutorials/index.html

d. OpenMM manual: http://docs.openmm.org/latest/userguide/index.html