Hydrocarbons in AMBER-ii Force Field

Alkanes force field [1] in AMBER-ii designed as a separate entity independent of the further intention of using it as part of a force field for proteins. This intention was expressed only in the choice of a simple functional form, traditional for biochemical force fields. Despite the simplicity, AMBER-ii gives quite accurate results both on conformational and thermodynamic properties of liquids.

Conformational properties on the example of cyclooctane

C8H16 boat-chair EAMBER-ii = 13.2816 kcal/mol	C8H16 crown EAMBER-ii = 15.4775 kcal/mol

Cyclooctane is a molecule that has large conformational flexibility but no “relaxed” state. “Boat-chair“ is a global energy minimum. Estimation of the energy difference between the “boat-chair“ and the "crown" conformation according to the quantum-chemical calculations MP2/6-311+G(2d,p) is 2.45 kcal/mol, in AMBER-ii 2.20 kcal/mol, in AMBER99 1.58 kcal/mol and in AMBER94 0.12 kcal/mol. Other examples are given in the article [1].

Thermodynamic properties

With the development of force fields for long linear alkanes a long history is associated. It is not easy to balance the FF so that the heats of evaporation of liquids correspond to the experimental values for long and short normal alkanes, as well as for branched ones.

In AMBER-ii, this is achieved due to the dependence of the Lennard-Jones parameters of carbon on the degree of its substitution¹. It should be noted that article data were obtained by the molecular dynamics method which can give an error of up to 0.5% depending on the type of integrator chosen and the step length. If accurate thermodynamic results are required, then it is better to use Monte Carlo methods. They work slower, but do not give systematic errors depending on the length of the step. In Abalone a xHMC method² is implemented whose efficiency approximately corresponds to the Verlet integrator in molecular dynamics.

¹ Alexei M. Nikitin, Yury V. Milchevskiy and Alexander P. Lyubartsev A new AMBER-compatible force field parameter set for alkanes. J Mol Model (2014) 20:2143 DOI 10.1007/s00894-014-2143-6

² C.M. Campos and J.M. Sanz-Serna Extra Chance Generalized Hybrid Monte Carlo. J. Comp. Phys. 281 (2015). DOI 10.1016/j.jcp.2014.09.037