Massively Parallel Implementation of Divide-and-Conquer Jacobi Iterations Using Particle-Mesh Ewald for Force Field Polarization

2018 ◽  
Vol 14 (7) ◽  
pp. 3633-3642 ◽  
Author(s):  
Dominique Nocito ◽  
Gregory J. O. Beran
Keyword(s):  
Force Field ◽  
Parallel Implementation ◽  
Divide And Conquer ◽  
Massively Parallel ◽  
Particle Mesh Ewald ◽  
Field Polarization ◽  
Jacobi Iterations

Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems

2019 ◽  
Author(s):  
Frédéric Célerse ◽  
Louis Lagardere ◽  
Étienne Derat ◽  
Jean-Philip Piquemal
Keyword(s):  
Molecular Dynamics ◽  
Parallel Implementation ◽  
Steered Molecular Dynamics ◽  
Massively Parallel

This paper is dedicated to the massively parallel implementation of Steered Molecular Dynamics in the Tinker-HP softwtare. It allows for direct comparisons of polarizable and non-polarizable simulations of realistic systems.

Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems

2019 ◽  
Author(s):  
Frédéric Célerse ◽  
Louis Lagardere ◽  
Étienne Derat ◽  
Jean-Philip Piquemal
Keyword(s):  
Molecular Dynamics ◽  
Parallel Implementation ◽  
Steered Molecular Dynamics ◽  
Massively Parallel

This paper is dedicated to the massively parallel implementation of Steered Molecular Dynamics in the Tinker-HP softwtare. It allows for direct comparisons of polarizable and non-polarizable simulations of realistic systems.

scholarly journals Combining experimental and simulation data of molecular processes via augmented Markov models

2017 ◽  
Vol 114 (31) ◽  
pp. 8265-8270 ◽  
Author(s):  
Simon Olsson ◽  
Hao Wu ◽  
Fabian Paul ◽  
Cecilia Clementi ◽  
Frank Noé
Keyword(s):  
Force Field ◽  
Structural Changes ◽  
Markov Models ◽  
Force Fields ◽  
Divide And Conquer ◽  
Simulation Data ◽  
Wide Range ◽  
Simulation And Experiment ◽  
Kinetics Of

Accurate mechanistic description of structural changes in biomolecules is an increasingly important topic in structural and chemical biology. Markov models have emerged as a powerful way to approximate the molecular kinetics of large biomolecules while keeping full structural resolution in a divide-and-conquer fashion. However, the accuracy of these models is limited by that of the force fields used to generate the underlying molecular dynamics (MD) simulation data. Whereas the quality of classical MD force fields has improved significantly in recent years, remaining errors in the Boltzmann weights are still on the order of a few kT, which may lead to significant discrepancies when comparing to experimentally measured rates or state populations. Here we take the view that simulations using a sufficiently good force-field sample conformations that are valid but have inaccurate weights, yet these weights may be made accurate by incorporating experimental data a posteriori. To do so, we propose augmented Markov models (AMMs), an approach that combines concepts from probability theory and information theory to consistently treat systematic force-field error and statistical errors in simulation and experiment. Our results demonstrate that AMMs can reconcile conflicting results for protein mechanisms obtained by different force fields and correct for a wide range of stationary and dynamical observables even when only equilibrium measurements are incorporated into the estimation process. This approach constitutes a unique avenue to combine experiment and computation into integrative models of biomolecular structure and dynamics.

Parallel algorithm for the identification of distributed scatterers in the problem of calculating the velocities of displacements of the earth’s surface by the Persistent Scaterrers method

2021 ◽  
pp. 82-97
Author(s):  
Семен Евгеньевич Попов ◽  
Вадим Петрович Потапов ◽  
Роман Юрьевич Замараев
Keyword(s):  
Parallel Implementation ◽  
General Scheme ◽  
Search Time ◽  
Identification Problem ◽  
Radar Data ◽  
Apache Spark ◽  
Massively Parallel ◽  
Maximization Problem ◽  
Homogeneous Sample ◽  
Entire Area

Описывается программная реализация быстрого алгоритма поиска распределенных рассеивателей для задачи построения скоростей смещений земной поверхности на базе платформы Apache Spark. Рассматривается полная схема расчета скоростей смещений методом постоянных рассеивателей. Предложенный алгоритм интегрируется в схему после этапа совмещения с субпиксельной точностью стека изображений временн´ой серии радарных снимков космического аппарата Sentinel-1. Алгоритм не является итерационным и может быть реализован в парадигме параллельных вычислений. Применяемая платформа Apache Spark позволила распределенно обрабатывать массивы стека радарных данных (от 60 изображений) в памяти на большом количестве физических узлов в сетевой среде. Время поиска распределенных рассеивателей удалось снизить в среднем до десяти раз по сравнению с однопроцессорной реализацией алгоритма. Приведены сравнительные результаты тестирования вычислительной системы на демонстрационном кластере. Алгоритм реализован на языке программирования Python c подробным описанием методов и объектов The article describes implementation of the software for a fast algorithm which finds distributed scatterers for the problem of plotting displacement velocities of the earth’s surface based on the Apache Spark platform. The Persistent Scatterer (PS) method is widely used for estimating the displacement rates of the earth’s surface. It consists of the identification of coherent radar targets (interferogram pixels) that demonstrate high phase stability during the entire observation period. The most advanced algorithm for solving the identification problem is the SqueeSAR algorithm. It allows searching and processing Distributed Scatterers (DS) - specific reflectors, integrating them into the general scheme for calculating displacement velocities using the PS method. A careful analysis of the SqueeSAR algorithm has identified areas that are critical to its performance. The whole algorithm is based on an enumeration of the initial data, where nontrivial transformations are performed at each step. The stages of searching for adjacent points in the design window with multiple passes over the entire area of the image and solving the maximization problem when assessing the real values of the interferometric phases turned out to be noticeably costly. To speed up the processing of images, it is proposed to use the Apache Spark massively parallel computing platform. Specialized primitives (Resilient Distributed Data) for recurrent inmemory processing are available here. This provides multiple accesses to the radar data loaded into memory from each cluster node and allows logical dividing of the snapshot stack into subareas. Thus calculations are performed independently in massively parallel mode. Based on the SqueeSAR mathematical model, it is assumed that the radar image data and the calculated geophysical parameters calculated are common for each statistically homogeneous sample of nearby pixels. In accordance with this assumption, the uniformity (homogeneity) of the pixels is estimated within a given window. The search for distributed scatterers occurs independently by the sequence of shifts of the windows over the entire area of the image. The window is shifted along the width and height of the image with a step equal to the width and height of the window. Pairs of samples in the window are composed of vectors of complex pixel values in each of the N images. The validity of the Kolmogorov-Smirnov criterion is checked for each of the pairs. To estimate the values of the phases of homogeneous pixels, the maximization problem is solved. The method of maximum likelihood estimation (MLE) is considered. The construction of the correct MLE form is carried out by analyzing the statistical properties of the coherence matrix of all images using the complex Wishart distribution. The Apache Spark platform applied here permits processing of distributed radar data stack arrays in memory on a large number of physical nodes in a network environment. The average search time for distributed scatterers turned out to be 10 times less compared to the uniprocessor implementation of the algorithm. The algorithm is implemented in the Python programming language with a detailed description of the objects and methods of the algorithm. The proposed algorithm and its parallel implementation allows applying the developed approaches to other problems and types of satellite data for remote sensing of the earth from space

Fast Electrostatic Force and Moment Calculations in Multibody-Based Simulations of Coarse-Grained Biopolymers

2011 ◽  
Author(s):  
Mohammad Poursina ◽  
Jeremy Laflin ◽  
Kurt S. Anderson
Keyword(s):  
Force Field ◽  
Long Range ◽  
Electrostatic Force ◽  
Center Of Mass ◽  
Computational Cost ◽  
Field Approximation ◽  
The Body ◽  
Divide And Conquer ◽  
Coarse Grained ◽  
Coarse Grain

In molecular simulations, the dominant portion of the computational cost is associated with force field calculations. Herein, we extend the approach used to approximate long range gravitational force and the associated moment in spacecraft dynamics to the coulomb forces present in coarse grained biopolymer simulations. We approximate the resultant force and moment for long-range particle-body and body-body interactions due to the electrostatic force field. The resultant moment approximated here is due to the fact that the net force does not necessarily act through the center of mass of the body (pseudoatom). This moment is considered in multibody-based coarse grain simulations while neglected in bead models which use particle dynamics to address the dynamics of the system. A novel binary divide and conquer algorithm (BDCA) is presented to implement the force field approximation. The proposed algorithm is implemented by considering each rigid/flexible domain as a node of the leaf level of the binary tree. This substructuring strategy is well suited to coarse grain simulations of chain biopolymers using an articulated multibody approach.

Sign in / Sign up

Export Citation Format

Share Document