Establishing conditions for simulating hydrophobic solutes in electric fields by molecular dynamics

Abstract

Despite considerable effort over the last decade, the interactions between solutes and solvents in the presence of electric fields have not yet been fully understood. A very useful manner in which to study these systems is through the application of molecular dynamics (MD) simulations. However, a number of MD studies have shown a tremendous sensitivity of the migration rate of a hydrophobic solute to the treatment of the long range part of the van der Waals interactions. While the origin of this sensitivity was never explained, the mobility is currently regarded as an artifact of an improper simulation setup. We explain the spread in observed mobilites by performing extensive molecular dynamics simulations using the GROMACS software package on a system consisting of a model hydrophobic object (Lennard-Jones particle) immersed in water both in the presence and absence of a static electric field. We retrieve a unidirectional field-induced mobility of the hydrophobic object when the forces are simply truncated. Careful analysis of the data shows that, only in the specific case of truncated forces, a non-zero van der Waals force acts, on average, on the Lennard-Jones particle. Using the Stokes law we demonstrate that this force yields quantitative agreement with the field-induced mobility found within this setup. In contrast, when the treatment of forces is continuous, no net force is observed. In this manner, we provide a simple explanation for the previously controversial reports.

The good, the bad and the user in soft matter simulations

“…This study further suggested that the non-zero force was generated by water molecules belonging to the first two hydration shells. Although, the result is sufficient to conclude that a non-zero force is produced by simple truncation of vdW forces, understanding of water's first two hydration shells causing the non-zero forces has not been achieved [52].…”

“…A net flux of water has also been observed in an uncharged CNT under an applied uniform electric field [50]. In this case, artifacts related to the treatment of the long-range part of the van der Waals interactions have been reported [51,52]. In particular, Bonthuis et al [45] simulated CNTs with different Lennard-Jones (LJ) cutoff lengths and two different truncation schemes: 1) simple cutoff, which sets the force to zero and the LJ potential to a small constant value beyond a cutoff distance (rc).…”

“…The above results cast doubt over the correctness of the implementation of the simple LJ cutoff in the GROMACS package [45,51,54]. Milicevic constructed a minimal model to examine the sensitivity of the simple cutoff scheme to the choice of rc [52]. MD simulations of an uncharged spherical LJ particle in water, both in the presence and absence of an external electric field, were performed using GROMACS.…”