Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package

Seabra, Gustavo; Walker, Ross C.; Elstner, Marcus; Case, David A.; Roitberg, Adrián E.

doi:10.1021/jp070071l

Cited by 227 publications

(194 citation statements)

References 88 publications

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“…2,19,20 The approach we have chosen is quite different, in that we start from an ab initio-like model that reproduces DFT results very well without the use of parameters, and then identify where and quantify by how much the model breaks down when various approximations are introduced. This information is then used to motivate the design of new, computationally efficient, and physically realistic quantum models that retains high accuracy with only a minimal reliance on empirical parameters.…”

Section: Introductionmentioning

confidence: 99%

Density-functional expansion methods: Generalization of the auxiliary basis

Giese¹,

York²

2011

The Journal of Chemical Physics

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The formulation of density-functional expansion methods is extended to treat the second and higherorder terms involving the response density and spin densities with an arbitrary single-center auxiliary basis. The two-center atomic orbital products are represented by the auxiliary functions centered about those two atoms, and the mapping coefficients are determined from a local constrained variational procedure. This two-center variational procedure allows the mapping coefficients to be pretabulated and splined as a function of internuclear separation for efficient look up. The splines of mapping coefficients have a range no longer than that of the overlap integrals, and the auxiliary density appears as a single point-multipole expansion to all nonoverlapping atoms, thus allowing for the trivial implementation of a linear-scaling algorithm. The method is tested using Gaussian multipole expansions, and the effect of angular and radial completeness is explored. Several auxiliary basis sets are parametrized and compared to an auxiliary basis analogous to that used in the selfconsistent-charge density-functional tight-binding model, and the method is demonstrated to greatly improve the representation of the density response with respect to a reference expansion model that does not use an auxiliary basis.

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Section: Introductionmentioning

confidence: 99%

Density-functional expansion methods: Generalization of the auxiliary basis

Giese¹,

York²

2011

The Journal of Chemical Physics

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“…Hybrid QM/MM calculations: Classical MM methods lack the ability to treat fundamentally quantum processes, such as bond breaking/forming and charge fluctuations as a function of geometry, [36] but it is possible to treat a subsection of the system by QM methods and use a coupling potential to connect the MM and QM regions. This hybrid QM/MM approach is seamlessly integrated in the sander module of AMBER 11 [34] and also includes a complete treatment of long-range electrostatics by using a QM/MM modified PME method.…”

mentioning

confidence: 99%

Mechanistic Insight into the Catalytic Activity of ββα‐Metallonucleases from Computer Simulations: Vibrio vulnificus Periplasmic Nuclease as a Test Case

et al. 2011

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Using information from wild‐type and mutant Vibrio vulnificus nuclease (Vvn) and I‐PpoI homing endonuclease co‐crystallized with different oligodeoxynucleotides, we have built the complex of Vvn with a DNA octamer and carried out a series of simulations to dissect the catalytic mechanism of this metallonuclease in a stepwise fashion. The distinct roles played in the reaction by individual active site residues, the metal cation and water molecules have been clarified by using a combination of classical molecular dynamics simulations and quantum mechanical calculations. Our results strongly support the most parsimonious catalytic mechanism, namely one in which a single water molecule from bulk solvent is used to cleave the phosphodiester bond and protonate the 3′‐hydroxylate leaving group.

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“…The expression on the right-hand side of AMBER force fields functional form is described in detail as follows: [14,15] (i) Summation over bonds is the first term, used to calculate the energy of the atoms that are bonded covalently. This harmonic force is also known as ideal spring force.…”

Section: Vs Of Big Datamentioning

confidence: 99%

Augmenting High-Performance Mobile Cloud Computations for Big Data in AMBER

Iqbal

Ali

Alfawair

et al. 2018

Wireless Communications and Mobile Computing

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Big data is an inspirational area of research that involves best practices used in the industry and academia. Challenging and complex systems are the core requirements for the data collation and analysis of big data. Data analysis approaches and algorithms development are the necessary and essential components of the big data analytics. Big data and high-performance computing emergent nature help to solve complex and challenging problems. High-Performance Mobile Cloud Computing (HPMCC) technology contributes to the execution of the intensive computational application at any location independently on laptops using virtual machines. HPMCC technique enables executing computationally extreme scientific tasks on a cloud comprising laptops. Assisted Model Building with Energy Refinement (AMBER) with the force fields calculations for molecular dynamics is a computationally hungry task that requires high and computational hardware resources for execution. The core objective of the study is to deliver and provide researchers with a mobile cloud of laptops capable of doing the heavy processing. An innovative execution of AMBER with force field empirical formula using Message Passing Interface (MPI) infrastructure on HPMCC is proposed. It is homogeneous mobile cloud platform comprising a laptop and virtual machines as processors nodes along with dynamic parallelism. Some processes can be executed to distribute and run the task among the various computational nodes. This task-based and databased parallelism is achieved in proposed solution by using a Message Passing Interface. Trace-based results and graphs will present the significance of the proposed method.

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Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package

Cited by 227 publications

References 88 publications

Density-functional expansion methods: Generalization of the auxiliary basis

Density-functional expansion methods: Generalization of the auxiliary basis

Mechanistic Insight into the Catalytic Activity of ββα‐Metallonucleases from Computer Simulations: Vibrio vulnificus Periplasmic Nuclease as a Test Case

Augmenting High-Performance Mobile Cloud Computations for Big Data in AMBER

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