Free Energy Landscapes of Alanine Dipeptide in Explicit Water Reproduced by the Force-Switching Wolf Method

Abstract

Precise and rapid calculation of long-range interactions is of crucial importance for molecular dynamics (MD) and Monte Carlo simulations. Instead of the Ewald method or its high speed variant, PME, we applied our novel method, called the force-switching Wolf method, to computation of the free energy landscapes of a short peptide in explicit water. Wolf and co-workers showed that long-range electrostatic energy under a periodic boundary condition can be well reproduced even by truncating the contribution from the distant charges, when the charge neutrality is taken into account. We recently applied the procedure proposed by Wolf and co-workers to a mathematically consistent MD theory by means of a force-switching scheme, and we show that the total electrostatic energy for sodium chloride liquid was well conserved and stable during the MD simulation with the force-switching Wolf method. Our current results for an aqueous peptide solution with a series of canonical and multicanonical molecular dynamics simulations show that the force-switching Wolf method is not only in good accordance with the energies and forces calculated by the conventional PME method but also properly reproduces the solvation and the free energy landscapes of the peptide at 300 K.

Non-Ewald methods: theory and applications to molecular systems

“…(11) is recovered as r 1  →  r c ). It was applied to calculate the free energies of an alanine dipeptide in explicit water, and reliable results were obtained (Yonezawa et al 2011). …”

“…Once the problems of the artifact and the accuracy are solved, the CB method could be more widely used because of its simplicity omitting the long range part of the interactions (Kikugawa et al 2009; Yonezawa et al 2011) and the irrelevance to boundary conditions.…”

Single‐pass incremental force updates for adaptively restrained molecular dynamics

“…In many simulations, most of the time is spent computing non‐bonded forces, typically divided into long‐range and short‐range forces. Long‐range interactions involve electrostatic interactions that are generally computed using specialized methods, including the reaction field method, the cell‐multipole method, the fast multipole method, particle Mesh Ewald, or the Wolf method . Short‐range forces decay fast and are generally truncated at a cut‐off distance r c .…”

“…These forces are efficiently computed using neighbor lists. With the Wolf method, long‐range forces may also be computed using neighbor lists, and this method recently attracted a great deal of attention for computing properties of electrolytes and simulating biomolecules in explicit solvent …”

Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations

“…On the practical aspect, the DSF methods have been demonstrated to reproduce well the static and dynamic properties for a number of non-reactive systems, including SPC/E water, 28 ionic molten salt systems, 28,36 polyelectrolyte brushes, 40 liquid-vapor interfaces, 41 and short peptides in explicit water. 42 These studies have provided positive motivation for making the DSF treatment compatible with QM/MM potentials for simulating reactive systems.…”