Revision of FMM–Yukawa: An adaptive fast multipole method for screened Coulomb interactions

Zhang, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai

doi:10.1016/j.cpc.2010.09.012

Cited by 6 publications

(7 citation statements)

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“…[1] the C++ software KIFMM developed by Ying et al [22] using a kernel-independent adaptive FMM was used. In this work, however, we adopt the Fortran software FMM-Yukawa developed by Huang et al [7,8] using the new version of the adaptive FMM that uses plane wave expansions to diagonalize the multipole-to-local translations. The program and its full description are available at http://www.fastmultipole.org/.…”

Section: Overview Of the Icsm And Its Theoretical Backgroundmentioning

confidence: 99%

“…In this model, solute molecules are placed in a central spherical cavity filled with explicit water, while the solvent outside the cavity is modeled as a dielectric continuum whose effect on the solute is treated through reaction field corrections. For improved computational efficiency, an accurate and efficient multiple-image charge method is used to compute these reaction field corrections [1–4], and at the same time the adaptive fast multipole method (FMM) [5–8] is employed to calculate the electrostatic force field inside the simulation box, including the direct Coulomb interactions between the explicit particles. When there are N charges inside the cavity, the use of the FMM will result in a speedup from O ( N log N ) for the Particle Mesh Ewald (PME) to only O ( N ) operations.…”

Section: Introductionmentioning

confidence: 99%

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

Baker¹,

Baumketner²,

Lin³

et al. 2013

Computer Physics Communications

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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.

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Section: Overview Of the Icsm And Its Theoretical Backgroundmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Baker¹,

Baumketner²,

Lin³

et al. 2013

Computer Physics Communications

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show abstract

“…[9] the C++ software KIFMM developed by Ying et al [66] using a kernel-independent adaptive FMM was used. However, in this work we adopt the Fortran software FMM-Yukawa developed by Huang et al [67,68] using the new version of the adaptive FMM that uses exponential expansions to diagonalize the multipole-to-local translations. The program and its full description are available at http://www.fastmultipole.org/.…”

Section: Numerical Examplesmentioning

confidence: 99%

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

Deng

Xue

Baumketner

et al. 2013

Journal of Computational Physics

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This paper extends the image charge solvation model (ICSM) [J. Chem. Phys. 131, 154103 (2009)], a hybrid explicit/implicit method to treat electrostatic interactions in computer simulations of biomolecules formulated for spherical cavities, to prolate spheroidal and triaxial ellipsoidal cavities, designed to better accommodate non-spherical solutes in molecular dynamics (MD) simulations. In addition to the utilization of a general truncated octahedron as the MD simulation box, central to the proposed extension is an image approximation method to compute the reaction field for a point charge placed inside such a non-spherical cavity by using a single image charge located outside the cavity. The resulting generalized image charge solvation model (GICSM) is tested in simulations of liquid water, and the results are analyzed in comparison with those obtained from the ICSM simulations as a reference. We find that, for improved computational efficiency due to smaller simulation cells and consequently a less number of explicit solvent molecules, the generalized model can still faithfully reproduce known static and dynamic properties of liquid water at least for systems considered in the present paper, indicating its great potential to become an accurate but more efficient alternative to the ICSM when bio-macromolecules of irregular shapes are to be simulated.

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“…Once the image charges are generated, pairwise forces between all source and all image charges must be summed. The ICSM performs this sum efficiently, scaling as O ( N ), using recent and very efficient FMM implementations [41–43]. …”

Section: Image Charge Solvation Model (Icsm)mentioning

confidence: 99%

Effect of the Reaction Field on Molecular Forces and Torques Revealed by an Image-Charge Solvation Model

Song

Lin

Baumketner

et al. 2013

Commun. comput. phys.

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We recently developed the Image-Charge Solvation Model (ICSM), which is an explicit/implicit hybrid model to accurately account for long-range electrostatic forces in molecular dynamics simulations [Lin et al., J. Chem. Phys., 131, 154103, 2009]. The ICSM has a productive spherical volume within the simulation cell for which key physical properties of bulk water are reproduced, such as density, radial distribution function, diffusion constants and dielectric properties. Although the reaction field (RF) is essential, it typically accounts for less than 2% of the total electrostatic force on a water molecule. This observation motivates investigating further the role of the RF within the ICSM. In this report we focus on distributions of forces and torques on water molecules as a function of distance from the origin and make extensive tests over a range of model parameters where Coulomb forces are decomposed into direct interactions from waters modeled explicitly and the RF. Molecular torques due to the RF typically account for 20% of the total torque, revealing why the RF plays an important role in the dielectric properties of simulated water. Moreover, it becomes clear that the buffer layer in the ICSM is essential to mitigate artifacts caused by the discontinuous change in dielectric constants at the explicit/implicit interface.

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Revision of FMM–Yukawa: An adaptive fast multipole method for screened Coulomb interactions

Cited by 6 publications

References 0 publications

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

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

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

Effect of the Reaction Field on Molecular Forces and Torques Revealed by an Image-Charge Solvation Model

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