Design of a reaction field using a linear‐combination‐based isotropic periodic sum method

Abstract

In our previous study (Takahashi et al., J. Chem. Theory Comput. 2012, 8, 4503), we developed the linear-combination-based isotropic periodic sum (LIPS) method. The LIPS method is based on the extended isotropic periodic sum theory that produces a ubiquitous interaction potential function to estimate homogeneous and heterogeneous systems. The LIPS theory also provides the procedure to design a periodic reaction field. To demonstrate this, in the present work, a novel reaction field of the LIPS method was developed. The novel reaction field was labeled LIPS-SW, because it provides an interaction potential function with a shape that resembles that of the switch function method. To evaluate the ability of the LIPS-SW method to describe in homogeneous and heterogeneous systems, we carried out molecular dynamics (MD) simulations of bulk water and water-vapor interfacial systems using the LIPS-SW method. The results of these simulations show that the LIPS-SW method gives higher accuracy than the conventional interaction potential function of the LIPS method. The accuracy of simulating water-vapor interfacial systems was greatly improved, while that of bulk water systems was maintained using the LIPS-SW method. We conclude that the LIPS-SW method shows great potential for high-accuracy, high-performance computing to allow large scale MD simulations. © 2014 Wiley Periodicals, Inc.

Truncation Effects of Shift Function Methods in Bulk Water Systems

“…Some reports on the accuracy of the IPS method of homogeneous [48,[50][51][52][53][54] and heterogeneous systems [47,50,[55][56][57] show that the method yields estimates in good agreement with the results of the Ewald sum. Improved methods were developed to speed up calculations for large-scale systems [58] and to improve the accuracy for homogeneous and heterogeneous systems [59,60].…”

A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water

“…Although many cutoff methods are pairwise, they cannot provide accurate free energies, which is crucial for the study of state equilibrium. IPS is as simple as any cutoff method, but, as accurate as PME [ 25 – 32 ]. To demonstrate the accuracy of IPS potential, we calculated the deprotonation free energies of the model compounds.…”

Critical test of isotropic periodic sum techniques with group-based cut-off schemes

“…The isotropic periodic sum (IPS) method developed by Wu and Brooks 31 is an advanced truncation method that can effectively reduce the computational cost while maintaining adequate accuracy to estimate many types of molecular system. To date, IPS techniques have been applied to many systems: solids 32 , liquids 31 , 33 – 39 , liquid–vapour interfaces 38 – 43 , solid–liquid interfaces 44 , 45 , phospholipid monolayers 46 , proteins 31 , 47 , combined quantum-mechanics/molecular-mechanics methods 48 , solid–liquid crystalline phase-transitions 49 , 50 and constant-pH MD simulations 14 – 16 . Those studies suggest that IPS techniques can be applied to many macromolecular systems and that they give reasonable results.…”

“…Those studies suggest that IPS techniques can be applied to many macromolecular systems and that they give reasonable results. To attain better computational accuracy than that of the original IPS method, a linear-combination-based IPS (LIPS) method 38 , 39 has been developed. In LIPS, several versions of pair potentials, LIPS-5th 38 , LIPS-SW 39 and so on were designed.…”

“…To attain better computational accuracy than that of the original IPS method, a linear-combination-based IPS (LIPS) method 38 , 39 has been developed. In LIPS, several versions of pair potentials, LIPS-5th 38 , LIPS-SW 39 and so on were designed. Our previous study showed that LIPS-SW is almost as accurate as PME with fine grid spacing (<0.1 nm) when used to estimate solid–liquid crystalline phase-transition temperatures 50 .…”