Evidence map›Paper›PMID 26395695›Full record

ArticleThe Journal of chemical physics2015

Generalized and efficient algorithm for computing multipole energies and gradients based on Cartesian tensors.

Dejun Lin

Abstract read
In one paragraph

Article in The Journal of chemical physics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

Who cites it

6 citing papers in PubMed.

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4 · The record

Corrections and comments

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5 · Who and what money

Authors and funding

1 author.

Dejun LinDepartment of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA.

Funding

Multiscale modeling of G protein-coupled receptorsR01GM095496 · NIGMS · UNIVERSITY OF ROCHESTER · PI GROSSFIELD, ALAN · 2011 to 2015
$1.3M
NIGMS NIH HHS GM095496NIGMS NIH HHS R01 GM095496
6 · The paper itself

Abstract

Accurate representation of intermolecular forces has been the central task of classical atomic simulations, known as molecular mechanics. Recent advancements in molecular mechanics models have put forward the explicit representation of permanent and/or induced electric multipole (EMP) moments. The formulas developed so far to calculate EMP interactions tend to have complicated expressions, especially in Cartesian coordinates, which can only be applied to a specific kernel potential function. For example, one needs to develop a new formula each time a new kernel function is encountered. The complication of these formalisms arises from an intriguing and yet obscured mathematical relation between the kernel functions and the gradient operators. Here, I uncover this relation via rigorous derivation and find that the formula to calculate EMP interactions is basically invariant to the potential kernel functions as long as they are of the form f(r), i.e., any Green's function that depends on inter-particle distance. I provide an algorithm for efficient evaluation of EMP interaction energies, forces, and torques for any kernel f(r) up to any arbitrary rank of EMP moments in Cartesian coordinates. The working equations of this algorithm are essentially the same for any kernel f(r). Recently, a few recursive algorithms were proposed to calculate EMP interactions. Depending on the kernel functions, the algorithm here is about 4-16 times faster than these algorithms in terms of the required number of floating point operations and is much more memory efficient. I show that it is even faster than a theoretically ideal recursion scheme, i.e., one that requires 1 floating point multiplication and 1 addition per recursion step. This algorithm has a compact vector-based expression that is optimal for computer programming. The Cartesian nature of this algorithm makes it fit easily into modern molecular simulation packages as compared with spherical coordinate-based algorithms. A software library based on this algorithm has been implemented in C++11 and has been released.

Indexed as

AlgorithmsModels, MolecularMolecular Dynamics SimulationNumerical Analysis, Computer-AssistedStatic Electricity

Identifiers

PMID26395695
PMCPMC4583518

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.