Achieving an Order of Magnitude Speedup in Hybrid-Functional- and Plane-Wave-Based <i>Ab Initio</i> Molecular Dynamics: Applications to Proton-Transfer Reactions in Enzymes and in Solution

Mandal, Sagarmoy; Thakkur, Vaishali; Nair, Nisanth N.

doi:10.1021/acs.jctc.1c00009

Cited by 17 publications

(38 citation statements)

References 99 publications

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“…This method is suited to study systems with broad, flat, and unbound free energy landscapes. This method has been applied to study various problems 59–64 and has also been extended to deal with high‐dimensional CV‐space 47 . By combining REST2 with WSMTD, we hope to boost the sampling of hidden transverse coordinates while exploring the relevant CV space.…”

Section: Introductionmentioning

confidence: 99%

Boosting the conformational sampling by combining replica exchange with solute tempering and well‐sliced metadynamics

Kapakayala

Nair

2021

J Comput Chem

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Methods that combine collective variable (CV) based enhanced sampling and global tempering approaches are used in speeding‐up the conformational sampling and free energy calculation of large and soft systems with a plethora of energy minima. In this paper, a new method of this kind is proposed in which the well‐sliced metadynamics approach (WSMTD) is united with replica exchange with solute tempering (REST2) method. WSMTD employs a divide‐and‐conquer strategy wherein high‐dimensional slices of a free energy surface are independently sampled and combined. The method enables one to accomplish a controlled exploration of the CV‐space with a restraining bias as in umbrella sampling, and enhance‐sampling of one or more orthogonal CVs using a metadynamics like bias. The new hybrid method proposed here enables boosting the sampling of more slow degrees of freedom in WSMTD simulations, without the need to specify associated CVs, through a replica exchange scheme within the framework of REST2. The high‐dimensional slices of the probability distributions of CVs computed from the united WSMTD and REST2 simulations are subsequently combined using the weighted histogram analysis method to obtain the free energy surface. We show that the new method proposed here is accurate, improves the conformational sampling, and achieves quick convergence in free energy estimates. We demonstrate this by computing the conformational free energy landscapes of solvated alanine tripeptide and Trp‐cage mini protein in explicit water.

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Section: Introductionmentioning

confidence: 99%

Boosting the conformational sampling by combining replica exchange with solute tempering and well‐sliced metadynamics

Kapakayala

Nair

2021

J Comput Chem

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“…have recently proposed a novel strategy, named s–MTACE, which provides the opportunity of performing around tenfold faster hybrid DFT‐based MD simulations of large condensed matter systems by analyzing trajectories. [ 29 ]…”

Section: Introductionmentioning

confidence: 99%

Benchmarking the Computational Costs and Quality of Vibrational Spectra from Ab Initio Simulations

Taherivardanjani¹,

Elfgen²,

Reckien³

et al. 2021

Advcd Theory and Sims

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The scaling behavior of ab initio molecular dynamics simulations for the different size bulk systems of liquid methanol is presented and thereby the characteristics of every system performing on either a local compute cluster or a supercomputer are analyzed. Additionally, the influence of different parameters on the quality of the infrared and Raman spectra is investigated using different simulation frameworks, including time step, convergence criteria, density functional approximation, and basis set. Both the maximally localized Wannier functions and the radical Voronoi tessellation approaches are employed to evaluate vibrational spectra from the trajectories. The results of infrared and Raman spectra are classified in two frequency regions, 500 to 1600 cm−1 and 2500 to 4000 cm−1, in order to compare and discuss the experimental spectra and the results derived from ab initio molecular dynamics simulations comprehensively. The outcome of this study guides future experimental and theoretical researchers in order to acquire a profound perception into vibrational spectra, which evolves the way of elucidating molecular structure.

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“…These methods could speed-up the calculations up to an order of magnitude without compromising on accuracy. 29,30,45 Both MTACE and s-MTACE methods are found to reproduce the structure and dynamics of bulk water and free energetics of chemical reactions in solutions correctly.…”

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confidence: 96%

“…The first set of techniques introduces some approximations in the evaluation of the HF exchange energy, thereby reducing the computational cost. Several works have been reported in this direction using localized orbitals, 16,[25][26][27]31,[33][34][35][36][37][38][39][40][41] multiple time step (MTS) algorithms, 29,30,[42][43][44][45] coordinate scaling, 46,47 and other strategies. [48][49][50][51] The other group of methods improve the performance by employing massively parallel algorithms.…”

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confidence: 99%

“…This approach provided a significant speed-up in AIMD simulations by decreasing the number of HF exchange evaluations. Subsequently, we improved the efficiency of this method 30 by employing localized orbitals. In particular, we used the selected columns of the density matrix (SCDM) 58 method to obtain localized orbitals, and we used these localized orbitals to build the ACE operator.…”

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Improving the scaling and performance of multiple time stepping‐based molecular dynamics with hybrid density functionals

et al. 2022

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Density functionals at the level of the generalized gradient approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) simulations. Going up in the ladder of accuracy of density functionals from GGA (second rung) to hybrid density functionals (fourth rung) is much desired pertaining to the accuracy of the latter in describing structure, dynamics, and energetics of molecular and condensed matter systems. On the other hand, hybrid density functional based AIMD simulations are about two orders of magnitude slower than GGA based AIMD for systems containing $100 atoms using $100 compute cores. Two methods, namely MTACE and s-MTACE, based on a multiple time step integrator and adaptively compressed exchange operator formalism are able to provide a speed-up of about 7-9 in performing hybrid density functional based AIMD. In this work, we report an implementation of these methods using a task-group based parallelization within the CPMD program package, with the intention to take advantage of the large number of compute cores available on modern high-performance computing platforms. We present here the boost in performance achieved through this algorithm.

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Achieving an Order of Magnitude Speedup in Hybrid-Functional- and Plane-Wave-Based Ab Initio Molecular Dynamics: Applications to Proton-Transfer Reactions in Enzymes and in Solution

Cited by 17 publications

References 99 publications

Boosting the conformational sampling by combining replica exchange with solute tempering and well‐sliced metadynamics

Boosting the conformational sampling by combining replica exchange with solute tempering and well‐sliced metadynamics

Benchmarking the Computational Costs and Quality of Vibrational Spectra from Ab Initio Simulations

Improving the scaling and performance of multiple time stepping‐based molecular dynamics with hybrid density functionals

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