Are Gaming-Enabled Graphic Processing Unit Cards Convenient for Molecular Dynamics Simulation?

Biagini, Tommaso; Petrizzelli, Francesco; Truglio, Mauro; Cespa, Roberto; Barbieri, Alessandro; Capocefalo, Daniele; Castellana, Stefano; Tevy, María Florencia; Carella, Massimo; Mazza, Tommaso

doi:10.1177/1176934319850144

Cited by 19 publications

(15 citation statements)

References 9 publications

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“…In parallel, we selected the putatively co-varying pairs of residues, where at least one of the pairs was reported as pathogenic in MITOMAP, and both were located in the interaction interface of proteins belonging to the same RC complex. We mapped these residues onto the 3D structure of the human RC I transmembrane arm and investigated the interacting properties of the wild-type complex and the single and double-mutated complexes for all the possible amino acids combinations of each co-varying pair through 50 ns-long molecular dynamics simulations performed using AMBER 18 ( 63 ), as described in ( 64 , 65 ). The root-mean-square deviation (RMSD), root mean square fluctuation (RMSF), binding energy components and per-residue hydrogen bonds were measured on the simulated trajectories using GROMACS 4.5 ( 66 ) and the g_mmpbsa package ( 67 ).…”

Section: Methodsmentioning

confidence: 99%

MitImpact 3: modeling the residue interaction network of the Respiratory Chain subunits

Castellana

Biagini

Petrizzelli

et al. 2020

Nucleic Acids Research

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Numerous lines of evidence have shown that the interaction between the nuclear and mitochondrial genomes ensures the efficient functioning of the OXPHOS complexes, with substantial implications in bioenergetics, adaptation, and disease. Their interaction is a fascinating and complex trait of the eukaryotic cell that MitImpact explores with its third major release. MitImpact expands its collection of genomic, clinical, and functional annotations of all non-synonymous substitutions of the human mitochondrial genome with new information on putative Compensated Pathogenic Deviations and co-varying amino acid sites of the Respiratory Chain subunits. It further provides evidence of energetic and structural residue compensation by techniques of molecular dynamics simulation. MitImpact is freely accessible at http://mitimpact.css-mendel.it.

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Section: Methodsmentioning

confidence: 99%

MitImpact 3: modeling the residue interaction network of the Respiratory Chain subunits

Castellana

Biagini

Petrizzelli

et al. 2020

Nucleic Acids Research

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“…The performance of newer versions (AMBER 18, GROMACS 2018, and NAMD 2.13) of the same software is investigated in a later article 203 of the same authors. This report focuses on graphics processors with the main question of whether gaming-oriented GPUs can be conveniently used for MD simulations or server-grade graphics hardware is necessary.…”

Section: Performance Comparison Of MD Software Packagesmentioning

confidence: 99%

Classical molecular dynamics on graphics processing unit architectures

Jász¹,

Rák²,

Ladjánszki³

et al. 2019

WIREs Comput Mol Sci

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Molecular dynamics (MD) has experienced a significant growth in the recent decades. Simulating systems consisting of hundreds of thousands of atoms is a routine task of computational chemistry researchers nowadays. Thanks to the straightforwardly parallelizable structure of the algorithms, the most promising method to speed‐up MD calculations is exploiting the large‐scale processing power offered by the parallel hardware architecture of graphics processing units or GPUs. Programming GPUs is becoming easier with general‐purpose GPU computing frameworks and higher levels of abstraction. In the recent years, implementing MD simulations on graphics processors has gained a large interest, with multiple popular software packages including some form of GPU‐acceleration support. Different approaches have been developed regarding various aspects of the algorithms, with important differences in the specific solutions. Focusing on published works in the field of classical MD, we describe the chosen implementation methods and algorithmic techniques used for porting to GPU, as well as how recent advances of GPU architectures will provide even more optimization possibilities in the future. This article is characterized under: Software > Simulation Methods Computer and Information Science > Computer Algorithms and Programming Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods

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“…Examples of that can be found in ab initio electronic structure calculations [21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40] but also in other areas such as classical molecular dynamics (MD). [41][42][43][44][45][46][47][48][49] One software in the first category is the QUantum Interaction Computational Kernel (QUICK) program. 31,32,37,38 QUICK is an open-source GPU-accelerated application capable of obtaining Hartree-Fock (HF) and density functional theory (DFT) energies and gradients and has a recently implemented multi-GPU functionality.…”

Section: Introductionmentioning

confidence: 99%

Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK

Cruzeiro¹,

Manathunga²,

Merz³

et al. 2021

Preprint

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<div><div><div><p>The quantum mechanics/molecular mechanics (QM/MM) approach is an essential and well-established tool in computational chemistry that has been widely applied in a myriad of biomolecular problems in the literature. In this publication, we report the integration of the QUantum Interaction Computational Kernel (QUICK) program as an engine to perform electronic structure calculations in QM/MM simulations with AMBER. This integration is available through either a file-based interface (FBI) or an application programming interface (API). Since QUICK is an open-source GPU-accelerated code with multi-GPU parallelization, users can take advantage of “free of charge” GPU-acceleration in their QM/MM simulations. In this work, we discuss implementation details and give usage examples. We also investigate energy conservation in typical QM/MM simulations performed at the microcanonical ensemble. Finally, benchmark results for two representative systems, the N-methylacetamide (NMA) molecule and the photoactive yellow protein (PYP) in bulk water, show the performance of QM/MM simulations with QUICK and AMBER using a varying number of CPU cores and GPUs. Our results highlight the acceleration obtained from a single or multiple GPUs; we observed speedups of up to 38x between a single GPU vs. a single CPU core and of up to 2.6x when comparing four GPUs to a single GPU. Results also reveal speedups of up to 3.5x when the API is used instead of FBI.</p></div></div></div>

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Are Gaming-Enabled Graphic Processing Unit Cards Convenient for Molecular Dynamics Simulation?

Cited by 19 publications

References 9 publications

MitImpact 3: modeling the residue interaction network of the Respiratory Chain subunits

MitImpact 3: modeling the residue interaction network of the Respiratory Chain subunits

Classical molecular dynamics on graphics processing unit architectures

Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK

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