Software & Data

All programs and data on this page are distributed in the hope that they will be useful to others, but we do not provide any support for installing and using them other than the included documentation.

Force Fields and Distributed Code on GitHub

Our GitHub site contains the most up to date versions of code and modified force fields which we have developed. These include:

• Code to determine diffusion coefficients and free energies from simulation data (diffit)
• Some public branches of plumed2
• Amber force fields optimized to match the helix-coil transition ff03*, ff99SB*, ff03w, ff99SBw
  • Robert B. Best and Gerhard Hummer. Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. J. Phys. Chem. B, 113:9004–9015, 2009.
  • Robert B. Best and Jeetain Mittal Protein simulations with an optimized water model: cooperative helix formation and temperature-induced unfolded state collapse. J. Phys. Chem. B, 114:14916-14923, 2010.
• Amber force field optimized to match residue-specific helix propensities: ff99SB*-ILDN-q
• Amber force fields with optimized protein-water interactions: ff03ws and ff99sbws
  • Robert B. Best, Wenwei Zheng and Jeetain Mittal Balanced protein-water interactions improve properties of disordered proteins and non-specific protein association. J. Chem. Theor. Comput., 10:5113-5124, 2014.
• GROMACS-formatted versions of most of the force fields are also now distributed via the contributed section of the GROMACS website.