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Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis

Junchao Xia, William F. Flynn, Emilio Gallicchio, Bin W. Zhang, Peng He, Zhiqiang Tan, Ronald M. Levy
2015 Journal of Computational Chemistry  
We describe methods to perform replica exchange molecular dynamics (REMD) simulations asynchronously (ASyncRE).  ...  The methods are designed to facilitate large scale REMD simulations on grid computing networks consisting of heterogeneous and distributed computing environments as well as on homogeneous high performance  ...  REMD simulations were carried out on the Gordon, Trestles, and Stampede clusters of XSEDE resources (supported by TG-MCB100145 and TG-MCB140124), and BOINC distributed networks at Temple University and  ... 
doi:10.1002/jcc.23996 pmid:26149645 pmcid:PMC4512903 fatcat:uoa3hkyil5atvod7rqzfwrmh6m

Characterization of the Three-Dimensional Free Energy Manifold for the Uracil Ribonucleoside from Asynchronous Replica Exchange Simulations

Brian K. Radak, Melissa Romanus, Tai-Sung Lee, Haoyuan Chen, Ming Huang, Antons Treikalis, Vivekanandan Balasubramanian, Shantenu Jha, Darrin M. York
2015 Journal of Chemical Theory and Computation  
However, daunting challenges remain in efficiently getting such simulations to scale to the very large number of replicas required to address problems in state spaces beyond two dimensions.  ...  Replica exchange molecular dynamics has emerged as a powerful tool for efficiently sampling free energy landscapes for conformational and chemical transitions.  ...  INTRODUCTION In the past few decades replica exchange molecular dynamics (REMD) has become one of the primary tools with which to improve the accuracy and efficiency of molecular simulations. 1 Examples  ... 
doi:10.1021/ct500776j pmid:26580900 pmcid:PMC4745604 fatcat:zhjjbahhnrfabaqkuhebs437cm

Asynchronous replica exchange software for grid and heterogeneous computing

Emilio Gallicchio, Junchao Xia, William F. Flynn, Baofeng Zhang, Sade Samlalsingh, Ahmet Mentes, Ronald M. Levy
2015 Computer Physics Communications  
Here we describe the architecture of a software (named ASyncRE) for performing asynchronous replica exchange molecular simulations on volunteered computing grids and heterogeneous high performance clusters  ...  Inter-process communication and coordination requirements have historically discouraged the deployment of replica exchange on distributed and heterogeneous resources.  ...  REMD simulations were carried out on the Stampede cluster of XSEDE (supported by TG-MCB100145 and TG-MCB140124), and BOINC distributed networks at Temple University and Brooklyn College of the City University  ... 
doi:10.1016/j.cpc.2015.06.010 pmid:27103749 pmcid:PMC4834714 fatcat:7nmcgpw73fezxebow5zmaqbhta

Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD

Wei Jiang, James C. Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James C. Gumbart, Yun Luo, Klaus Schulten, Benoît Roux
2014 Computer Physics Communications  
Widely used examples of MCAs include temperature and Hamiltonian-tempering replica-exchange molecular dynamics (T-REMD and H-REMD), alchemical free energy perturbation with lambda replica-exchange (FEP  ...  Here, we report a robust and general implementation of MCAs for molecular dynamics (MD) simulations in the highly scalable program NAMD built upon the parallel programming system Charm++.  ...  This work also is supported by the National Institutes of Health through grants 9P41GM104601 (K.S. and J.P.), U54GM087519 (K.S. and B.R.), and K22-AI100927 (J.C.G.) and by MCB-0920261 (B.R.) from the National  ... 
doi:10.1016/j.cpc.2013.12.014 pmid:24944348 pmcid:PMC4059768 fatcat:kdvuh47garbkvphytdkramlg7m

Federating Advanced Cyberinfrastructures with Autonomic Capabilities [chapter]

Javier Diaz-Montes, Ivan Rodero, Mengsong Zou, Manish Parashar
2014 Cloud Computing for Data-Intensive Applications  
Clouds provide on-demand access to computing utilities, an abstraction of unlimited computing resources, and support for ondemand scale up, scale down and scale out.  ...  As a result, providing scalable and robust mechanisms to federate distributed infrastructures and handle application workflows, that can effectively utilize them, is critical.  ...  Molecular Dynamics Simulations Using Asynchronous Replica Exchange Replica exchange [23, 64] is a powerful sampling algorithm that preserves canonical distributions and allows for efficient crossing  ... 
doi:10.1007/978-1-4939-1905-5_9 fatcat:eyuo5q37enaofehsubefabd7ky

Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field

Hujun Shen, Cezary Czaplewski, Adam Liwo, Harold A. Scheraga
2008 Journal of Chemical Theory and Computation  
The kinetic-trapping problem in simulating protein folding can be overcome by using a Replica Exchange Method (REM).  ...  With the temperature-independent force field, SREM reproduces the results of REM but is more efficient in terms of wall-clock time and scales better on distributed-memory machines.  ...  Plots of the weak scaling data, probed by holding the per-node computational work constant for Multiplexing Replica Exchange Molecular Dynamics (REM, squares) and Serial Replica Exchange Molecular Dynamics  ... 
doi:10.1021/ct800063d pmid:20011673 pmcid:PMC2790181 fatcat:n7umngytlvckngynohzhoonkpm

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

Cameron Abrams, Giovanni Bussi
2013 Entropy  
We review a selection of methods for performing enhanced sampling in molecular dynamics simulations.  ...  We then turn to methods that use bias potentials, including umbrella sampling and metadynamics. We next consider parallel tempering and replica-exchange methods.  ...  Since efficiency of parallel tempering simulation can deteriorate if the stride between subsequent exchanges is too large [192, 193] , a typical recipe is to choose this stride as small as possible, with  ... 
doi:10.3390/e16010163 fatcat:iqdr2qne3vcfjaovn3tjvcdlpi

Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation

Zhiqiang Tan, Junchao Xia, Bin W. Zhang, Ronald M. Levy
2016 Journal of Chemical Physics  
Articles you may be interested in On the rejection-based algorithm for simulation and analysis of large-scale reaction networks Fast variance reduction for steady-state simulation and sensitivity analysis  ...  To illustrate the methods, we estimated absolute binding free energies and binding energy distributions using the binding energy distribution analysis method from one and two dimensional replica exchange  ...  and performing Hamiltonian replica exchange in the λ space and more recently in the ASyncRE python package using asynchronous pairwise independence exchange scheme 45,46 for a multidimensional parameter  ... 
doi:10.1063/1.4939768 pmid:26801020 pmcid:PMC4729400 fatcat:ta76aihdijdfpkk5ga3jr3kuu4

Computational studies of transport in ion channels using metadynamics

Simone Furini, Carmen Domene
2016 Biochimica et Biophysica Acta - Biomembranes  
However, exhaustive sampling by standard molecular dynamics is in most cases computationally prohibitive, and the time scales accessible remain significantly shorter than many biological processes of interest  ...  In particular, in the study of ion channels, realistic models to describe permeation and gating require accounting for large numbers of particles and accurate interaction potentials, which severely limits  ...  Similarly, in BE-META, multiple replicas of the same system are employed and sampling is optimized by exchanging configurations among these replicas.  ... 
doi:10.1016/j.bbamem.2016.02.015 pmid:26891818 fatcat:pdhlrew2e5e7linocq7dw7krhq

Using collective variables to drive molecular dynamics simulations

Giacomo Fiorin, Michael L. Klein, Jérôme Hénin
2013 Molecular Physics  
The present modular software is extensible, and portable between commonly used MD simulation engines.  ...  A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations  ...  Acknowledgements The authors thank Klaus Schulten and James Phillips for their help in extending NAMD, and Christopher Harrison and Christophe Chipot for many constructive discussions.  ... 
doi:10.1080/00268976.2013.813594 fatcat:fbx4ezqcszavtbnitqutw2hmve

A combined treatment of hydration and dynamical effects for the modeling of host–guest binding thermodynamics: the SAMPL5 blinded challenge

Rajat Kumar Pal, Kamran Haider, Divya Kaur, William Flynn, Junchao Xia, Ronald M Levy, Tetiana Taran, Lauren Wickstrom, Tom Kurtzman, Emilio Gallicchio
2016 Journal of Computer-Aided Molecular Design  
exchange conformational sampling and the AGBNP2 implicit solvation model specifically customized to treat the effect of water displacement as modeled by the Hydration Site Analysis method with explicit  ...  The work validates the implicit/explicit solvation approach employed here and it shows that comprehensive physical models can be effective at predicting binding affinities of molecular complexes requiring  ...  REMD simulations were carried out on the Supermic cluster of XSEDE (supported by TG-MCB150001), and BOINC distributed networks at  ... 
doi:10.1007/s10822-016-9956-6 pmid:27696239 pmcid:PMC5477994 fatcat:fkklpq7bjjcy7llyfm2ti7yyh4

Multiscale Methods for Computational RNA Enzymology [chapter]

Maria T. Panteva, Thakshila Dissanayake, Haoyuan Chen, Brian K. Radak, Erich R. Kuechler, George M. Giambaşu, Tai-Sung Lee, Darrin M. York
2015 Methods in Enzymology  
Classical molecular dynamics (MD) simulations, reference interaction site model (RISM) calculations, constant pH molecular dynamics (CpHMD) simulations, Hamiltonian replica exchange molecular dynamics  ...  (HREMD) and quantum mechanical/molecular mechanical (QM/MM) simulations will be discussed in the context of the study of RNA backbone cleavage transesterification.  ...  ACI-0725070 and ACI-1238993, and the Minnesota Supercomputing Institute for Advanced Computational Research (MSI).  ... 
doi:10.1016/bs.mie.2014.10.064 pmid:25726472 pmcid:PMC4739856 fatcat:6sulkyhhtvhqjllibkk7qvlrsu

A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness

T. J. Sego, Josua O. Aponte-Serrano, Juliano Ferrari Gianlupi, Samuel R. Heaps, Kira Breithaupt, Lutz Brusch, Jessica Crawshaw, James M. Osborne, Ellen M. Quardokus, Richard K. Plemper, James A. Glazier, Shayn M. Peirce
2020 PLoS Computational Biology  
Many combinations of dosage and treatment time lead to stochastic outcomes, with some simulation replicas showing clearance or control (treatment success), while others show rapid infection of all epithelial  ...  We present an open-source platform for multiscale spatiotemporal simulation of an epithelial tissue, viral infection, cellular immune response and tissue damage, specifically designed to be modular and  ...  Smith for useful discussions and ideas and for comments on the manuscript.  ... 
doi:10.1371/journal.pcbi.1008451 pmid:33347439 fatcat:voro2enb6fgkbezzr2lzmnvtjy

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

Jiří Šponer, Giovanni Bussi, Miroslav Krepl, Pavel Banáš, Sandro Bottaro, Richard A. Cunha, Alejandro Gil-Ley, Giovanni Pinamonti, Simón Poblete, Petr Jurečka, Nils G. Walter, Michal Otyepka
2018 Chemical Reviews  
Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution.  ...  With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics  ...  Results are obtained using an asynchronous replica exchange US procedure where these three CVs are biased.  ... 
doi:10.1021/acs.chemrev.7b00427 pmid:29297679 pmcid:PMC5920944 fatcat:q3qxrwmofrfylakvsozxypkxhm

From Data to Knowledge: Systematic Review of Tools for Automatic Analysis of Molecular Dynamics Output

Hanna Baltrukevich, Sabina Podlewska
2022 Frontiers in Pharmacology  
Therefore, there are also more and more approaches that facilitate the analysis and interpretation of the results of structure-based tools.  ...  Docking and molecular dynamics simulations, key representatives of the structure-based approaches, provide detailed information about the potential interaction of a ligand with a target receptor.  ...  What is more, Desmond provides distinct panels for metadynamics and replica exchange simulations analysis, and Python scripts applicable for PCA, density profile calculations, and others.  ... 
doi:10.3389/fphar.2022.844293 pmid:35359865 pmcid:PMC8960308 fatcat:a5hw6tqawne3vg46scvjcxrg4u
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