Reconsidering Dispersion Potentials: Reduced Cutoffs in Mesh-Based Ewald Solvers Can Be Faster Than Truncation

Abstract

Long-range dispersion interactions have a critical influence on physical quantities in simulations of inhomogeneous systems. However, the perceived computational overhead of long-range solvers has until recently discouraged their implementation in molecular dynamics packages. Here, we demonstrate that reducing the cutoff radius for local interactions in the recently introduced particle-particle particle-mesh (PPPM) method for dispersion [Isele-Holder et al., J. Chem. Phys., 2012, 137, 174107] can actually often be faster than truncating dispersion interactions. In addition, because all long-range dispersion interactions are incorporated, physical inaccuracies that arise from truncating the potential can be avoided. Simulations using PPPM or other mesh Ewald solvers for dispersion can provide results more accurately and more efficiently than simulations that truncate dispersion interactions. The use of mesh-based approaches for dispersion is now a viable alternative for all simulations containing dispersion interactions and not merely those where inhomogeneities were motivating factors for their use. We provide a set of parameters for the dispersion PPPM method using either ik or analytic differentiation that we recommend for future use and demonstrate increased simulation efficiency by using the long-range dispersion solver in a series of performance tests on massively parallel computers.

Direct-Space Corrections Enable Fast and Accurate Lorentz–Berthelot Combination Rule Lennard-Jones Lattice Summation

“…The use of mesh-based solvers for all long-range interactions has been shown to transform the cutoff into a possible tuning parameter for performance. 17 Therefore, a force field parametrized with a correct treatment of all long-range interactions might remove the cutoff-restriction present in existing force fields, and thus we would obtain an accurate force field where the cutoff is used as an extra tuning parameter to achieve the highest performance. Tables Table 1: Calculated area per lipid from 100 ns simulations of POPC using LJ-PME.…”

“…For this reason a lot of work has been invested in further developing the general solution, derived by Ewald, 21 in order to also be applicable to molecular simulations. 1,2,15,17,[22][23][24] Following the derivation of Essman, 2 the expression above, applied to dispersion inter-actions, can be rewritten as…”

“…A recent suggestion by Isele-Holder et al, 17 regarding the applicable cutoffs when using long-range dispersion solvers, noted that cutoffs shorter than twice the largest LJ-diameter would impact the system properties since effects from the truncation of the repulsion term becomes non-negligible. For the DPPC-system studied here, the LJ-diameter of the methylene groups in the united atom tails is approximately 4.1Å, which suggests that results obtained with cutoffs lower than˜8.2Å would be innacurate to use.…”

“…lipid bilayers) is troublesome since the assumption that g(r) is equal to unity beyond the cutoff inherently assumes that the system is homogeneous and isotropic, something that most definitely is not true for these systems. The implication of this for simulations containing lipid bilayers has not been given much attention in the past, but coupled to the development of alternative ways of treating long-range LJ interactions [10][11][12][13][14][15][16][17] the problem has started to become more apparent the last few years. In light of this, we recently presented an implementation in the Gromacs simulation package where the PME method was used to calculate long-range LJ interactions.…”

Communication: Truncated non-bonded potentials can yield unphysical behavior in molecular dynamics simulations of interfaces

“…This is especially important in an interfacial simulation setting such as a slab, where a cutoff-caused change in interaction from the substrate side is not compensated by an equal change from the vacuum side. Consequently, only employing much larger cutoffs or techniques to calculate the long-range part of the dispersion force [37][38][39] can ensure that unphysical effects are avoided. A minimal sanity check for future wetting studies could be to start simulations from both a wetting film and a spherical liquid snapshot.…”