Off-the-shelf potentials

In an effort to counter the problem of developing a new forcefield every time a different MD simulation is to be performed, a variety of off-the-shelf potentials have been developed. These aspire to be general forcefields to be applied to any system.

Although these potential models are developed with the aim of generality, they should still be used with caution. The chemistry of your system may not directly match the system used in the potential generation, which can lead to systematic errors in your the simulations.

Some examples of off-the-shelf potentials include:

  • AMBER: popular for DNA and proteins [1]
  • CFF: designed for a broad variety of organic compounds [2]
  • CHARMM: widely used for small molecules [3]
  • GROMOS: common for biomolecular systems [4]
  • OPLS-AA: optimised for liquid simulations [5]

These can be applied to many systems, however, as mentioned above, they should be used with care. One way to assess the suitability of an off-the-shelf potential is to to reproduce a simple, but well-defined, property of the material, e.g. density.

References

  1. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117 (19), 5179–5197. 10.1021/ja00124a002.
  2. Lifson, S.; Warshel, J. Chem. Phys. 1968, 49 (11), 5116–5129. 10.1063/1.1670007.
  3. MacKerell, A. D.; Banavali, N.; Foloppe, N. Biopolymers 2000, 56 (4), 257–265. 10.1002/1097-0282(2000)56:4<257::AID-BIP10029>3.0.CO;2-W.
  4. Reif, M. M.; Winger, M.; Oostenbrink, C. J. Chem. Theory Comput. 2013, 9 (2), 1247–1264. 10.1021/ct300874c.
  5. Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110 (6), 1657–1666. 10.1021/ja00214a001.