scholarly journals Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems

2020 ◽  
Vol 16 (8) ◽  
pp. 4757-4775 ◽  
Author(s):  
Paraskevi Gkeka ◽  
Gabriel Stoltz ◽  
Amir Barati Farimani ◽  
Zineb Belkacemi ◽  
Michele Ceriotti ◽  
...  
Author(s):  
Jiang Wang ◽  
Simon Olsson ◽  
Christoph Wehmeyer ◽  
Adrià Pérez ◽  
Nicholas E. Charron ◽  
...  

2021 ◽  
Author(s):  
Xiangyun Lei ◽  
Andrew Medford

Abstract Molecular dynamics simulations are an invaluable tool in numerous scientific fields. However, the ubiquitous classical force fields cannot describe reactive systems, and quantum molecular dynamics are too computationally demanding to treat large systems or long timescales. Reactive force fields based on physics or machine learning can be used to bridge the gap in time and length scales, but these force fields require substantial effort to construct and are highly specific to a given chemical composition and application. A significant limitation of machine learning models is the use of element-specific features, leading to models that scale poorly with the number of elements. This work introduces the Gaussian multipole (GMP) featurization scheme that utilizes physically-relevant multipole expansions of the electron density around atoms to yield feature vectors that interpolate between element types and have a fixed dimension regardless of the number of elements present. We combine GMP with neural networks to directly compare it to the widely used Behler-Parinello symmetry functions for the MD17 dataset, revealing that it exhibits improved accuracy and computational efficiency. Further, we demonstrate that GMP-based models can achieve chemical accuracy for the QM9 dataset, and their accuracy remains reasonable even when extrapolating to new elements. Finally, we test GMP-based models for the Open Catalysis Project (OCP) dataset, revealing comparable performance to graph convolutional deep learning models. The results indicate that this featurization scheme fills a critical gap in the construction of efficient and transferable machine-learned force fields.


2019 ◽  
Vol 59 (10) ◽  
pp. 4278-4288 ◽  
Author(s):  
James L. McDonagh ◽  
Ardita Shkurti ◽  
David J. Bray ◽  
Richard L. Anderson ◽  
Edward O. Pyzer-Knapp

2006 ◽  
Vol 978 ◽  
Author(s):  
Sheng D. Chao

AbstractCurrent large scale atomistic simulations remain too computationally demanding to be generally applicable to industrial and bioengineering materials. It is desirable to develop multiscale modeling algorithms to perform efficient and informative mesoscopic simulations. Here we present a multipolar expansion method to construct coarse grained force fields (CGFF) for polymer nanostructures and nanocomposites. This model can effectively capture the stereochemical response to anisotropic long-range interactions and can be systematically improved upon adding higher order terms. The coarse-graining procedure forms the basis to perform a hierarchy of multiscale simulations starting with the quantum chemistry calculations to coarse grained molecular dynamics, hopefully toward continuum modeling. We have applied this procedure to molecular clusters such as alkane, benzene, and fullerene. For liquid alkane, molecular dynamics simulations using the CGFF can reproduce the pair distribution functions using atomistic force fields. Molecular mechanics simulations using the CGFF can well reproduce the energetics of benzene clusters from quantum chemistry electronic structure calculations. Subtle anisotropy in the interaction potentials of the fullerene dimer using the Brenner force field can also be well represented by the model. It is promising this procedure can be standardized and further extended.


2019 ◽  
Vol 20 (15) ◽  
pp. 3774 ◽  
Author(s):  
Nidhi Singh ◽  
Wenjin Li

Molecular dynamics simulations have emerged as a powerful tool to study biological systems at varied length and timescales. The conventional all-atom molecular dynamics simulations are being used by the wider scientific community in routine to capture the conformational dynamics and local motions. In addition, recent developments in coarse-grained models have opened the way to study the macromolecular complexes for time scales up to milliseconds. In this review, we have discussed the principle, applicability and recent development in coarse-grained models for biological systems. The potential of coarse-grained simulation has been reviewed through state-of-the-art examples of protein folding and structure prediction, self-assembly of complexes, membrane systems and carbohydrates fiber models. The multiscale simulation approaches have also been discussed in the context of their emerging role in unravelling hierarchical level information of biosystems. We conclude this review with the future scope of coarse-grained simulations as a constantly evolving tool to capture the dynamics of biosystems.


2021 ◽  
Author(s):  
Fréderic Célerse ◽  
Theo Jaffrelot-Inizan ◽  
Louis Lagardère ◽  
Olivier Adjoua ◽  
Pierre Monmarché ◽  
...  

We introduce a novel multi-level enhanced sampling strategy grounded on Gaussian accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs-accelerated implementation within the Tinker-HP molecular dynamics package. We introduce the new "dual-water" mode and its use with the flexible AMOEBA polarizable force field.By adding harmonic boosts to the water stretching and bonding terms, it accelerates the solvent-solute interactions while enabling speedups thanks to the use of fast multiple--timestep integrators. To further reduce time-to-solution, we couple GaMD to Umbrella Sampling (US). The GaMD—US/dual--water approach is tested on the 1D Potential of Mean Force (PMF) of the solvated CD2--CD58 system (168000 atoms) allowing the AMOEBA PMF to converge within 1 kcal/mol of the experimental value. Finally, Adaptive Sampling (AS) is added enabling AS-GaMD capabilities but also the introduction of the new Adaptive Sampling--US--GaMD (ASUS-GaMD) scheme. The highly parallel ASUS--GaMD setup decreases time to convergence by respectively 10 and 20 times compared to GaMD-US and US. Overall, beside the acceleration of PMF computations, Tinker-HP now allows for the simultaneous use of Adaptive Sampling and GaMD-"dual water" enhanced sampling approaches increasing the applicability of polarizable force fields to large scale simulations of biological systems.


Polymers ◽  
2021 ◽  
Vol 13 (16) ◽  
pp. 2683
Author(s):  
Takashi Kojima ◽  
Takashi Washio ◽  
Satoshi Hara ◽  
Masataka Koishi ◽  
Naoya Amino

A better understanding of the microstructure–property relationship can be achieved by sampling and analyzing a microstructure leading to a desired material property. During the simulation of filled rubber, this approach includes extracting common aggregates from a complex filler morphology consisting of hundreds of filler particles. However, a method for extracting a core structure that determines the rubber mechanical properties has not been established yet. In this study, we analyzed complex filler morphologies that generated extremely high stress using two machine learning techniques. First, filler morphology was quantified by persistent homology and then vectorized using persistence image as the input data. After that, a binary classification model involving logistic regression analysis was developed by training a dataset consisting of the vectorized morphology and stress-based class. The filler aggregates contributing to the desired mechanical properties were extracted based on the trained regression coefficients. Second, a convolutional neural network was employed to establish a classification model by training a dataset containing the imaged filler morphology and class. The aggregates strongly contributing to stress generation were extracted by a kernel. The aggregates extracted by both models were compared, and their shapes and distributions producing high stress levels were discussed. Finally, we confirmed the effects of the extracted aggregates on the mechanical property, namely the validity of the proposed method for extracting stress-contributing fillers, by performing coarse-grained molecular dynamics simulations.


Author(s):  
JCS Kadupitiya ◽  
Geoffrey C Fox ◽  
Vikram Jadhao

Simulating the dynamics of ions near polarizable nanoparticles (NPs) using coarse-grained models is extremely challenging due to the need to solve the Poisson equation at every simulation timestep. Recently, a molecular dynamics (MD) method based on a dynamical optimization framework bypassed this obstacle by representing the polarization charge density as virtual dynamic variables and evolving them in parallel with the physical dynamics of ions. We highlight the computational gains accessible with the integration of machine learning (ML) methods for parameter prediction in MD simulations by demonstrating how they were realized in MD simulations of ions near polarizable NPs. An artificial neural network–based regression model was integrated with MD simulation and predicted the optimal simulation timestep and optimization parameters characterizing the virtual system with 94.3% success. The ML-enabled auto-tuning of parameters generated accurate dynamics of ions for ≈ 10 million steps while improving the stability of the simulation by over an order of magnitude. The integration of ML-enhanced framework with hybrid Open Multi-Processing / Message Passing Interface (OpenMP/MPI) parallelization techniques reduced the computational time of simulating systems with thousands of ions and induced charges from thousands of hours to tens of hours, yielding a maximum speedup of ≈ 3 from ML-only acceleration and a maximum speedup of ≈ 600 from the combination of ML and parallel computing methods. Extraction of ionic structure in concentrated electrolytes near oil–water emulsions demonstrates the success of the method. The approach can be generalized to select optimal parameters in other MD applications and energy minimization problems.


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