Improving the Numerical Stability of the NAST Force Field for RNA Simulations

Abstract

The NAST force field is a popular tool for modeling RNA and is typical of low-resolution approaches. Unfortunately, some combinations of bond and dihedral angles can reach cliffs on the energy landscape which lead to numerical disasters. We describe changes to the formulation (NAST improved, NASTI) which smooth the dihedral energy term when neighboring angles become flat. We also improved the fit to experimental structures by replacing the harmonic term for the backbone angles with spline functions and using a more sophisticated approach to calculate energies for fragments that span both helix and loop regions. A newer, larger set of structures was used for the parametrization. The new formulation can be run for millions of steps without a thermostat, whereas NAST routinely suffers numerical catastrophes. Simulations with NASTI showed no decrease in the quality of the structures as reflected by slightly better GDT-TS scores and, in three of the five cases, marginally better RMSD values when compared to the crystal structures.