ICSM: An order method for calculating electrostatic interactions added to TINKER

Abstract

We present an order N method for calculating electrostatic interactions that has been integrated into the molecular dynamics portion of the TINKER Molecular Modeling package. This method, introduced in a previous paper [J. Chem. Phys. 131 (2009) 154103] and termed the Image-Charge Solvation Model (ICSM), is a hybrid electrostatic approach that combines the strengths of both explicit and implicit representations of the solvent. A multiple-image method is used to calculate reaction fields due to the implicit part while the Fast Multipole Method (FMM) is used to calculate the Coulomb interactions for all charges, including the explicit part. The integrated package is validated through test simulations of liquid water. The results are compared with those obtained by the Particle Mesh Ewald (PME) method that is built in the TINKER package. Timing performance of TINKER with the integrated ICSM is benchmarked on bulk water as a function of the size of the system. In particular, timing analysis results show that the ICSM outperforms the PME for sufficiently large systems with the break-even point at around 30,000 particles in the simulated system.

Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models

“…Finally, alternatives to continuum implicit solvent models exist, mainly in the form of hybrid models and molecular integral equation approaches, most prominently 3D‐reference site interaction models (RISMs), that more naturally avoid many of the assumptions of continuum approaches. While these have generally been too slow to provide much advantage over explicit models in the context of simulation, recent advances in hybrid models (both in the traditional explicit‐continuum implicit methods and in lattice methods) and in 3D‐RISMs are making them viable alternatives …”

Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions

“…On the other hand, while the ICSM/GICSM has a better asymptotic computational complexity O ( N ) than the O ( N log N ) complexity of the PME, when used to simulate homogeneous systems of relatively small sizes, the PME was found significantly more efficient. However, in a separate project [29], we also found that, when integrated into TINKER [30], the ICSM becomes computationally more efficient than the PME built into TINKER when 30,000 or more explicit atoms are included in the simulated system.…”

Investigating the Selectivity of KcsA Channel by an Image Charge Solvation Method (ICSM) in Molecular Dynamics Simulations

“…Due to the principle of superposition, we only need to consider the case of one single source charge in V in , i.e. ρ in (r) = qδ(r−r s ), and the total potential can be written as Φ = Φ S +Φ RF where Φ RF is the primary field that results from the source charge q at r s and Φ RF is the reaction field from the exterior dielectric medium with dielectric constant ε o and the inverse Debye-H ückel screening length λ = 0, respectively [1,24]. The reaction field can be approximated by a set of discrete image charges based on Gauss-Radau quadratures as [5]:…”