Literature DB >> 26616351

A Stochastic Algorithm for the Isobaric-Isothermal Ensemble with Ewald Summations for All Long Range Forces.

Michele Di Pierro1, Ron Elber2,3, Benedict Leimkuhler4.   

Abstract

We present an algorithm termed COMPEL (COnstant Molecular Pressure with Ewald sum for Long range forces) to conduct simulations in the NPT ensemble. The algorithm combines novel features recently proposed in the literature to obtain a highly efficient and accurate numerical integrator. COMPEL exploits the concepts of molecular pressure, rapid stochastic relaxation to equilibrium, exact calculation of the contribution to the pressure of long-range nonbonded forces with Ewald summation, and the use of Trotter expansion to generate a robust, highly stable, symmetric, and accurate algorithm. Explicit implementation in the MOIL program and illustrative numerical examples are discussed.

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Year:  2015        PMID: 26616351      PMCID: PMC4890727          DOI: 10.1021/acs.jctc.5b00648

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  13 in total

1.  Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations.

Authors:  Joseph E Basconi; Michael R Shirts
Journal:  J Chem Theory Comput       Date:  2013-06-03       Impact factor: 6.006

2.  Canonical sampling through velocity rescaling.

Authors:  Giovanni Bussi; Davide Donadio; Michele Parrinello
Journal:  J Chem Phys       Date:  2007-01-07       Impact factor: 3.488

3.  Accurate sampling using Langevin dynamics.

Authors:  Giovanni Bussi; Michele Parrinello
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2007-05-25

4.  Application of Ewald summations to long-range dispersion forces.

Authors:  Pieter J in't Veld; Ahmed E Ismail; Gary S Grest
Journal:  J Chem Phys       Date:  2007-10-14       Impact factor: 3.488

5.  Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure.

Authors:  Ross A Lippert; Cristian Predescu; Douglas J Ierardi; Kenneth M Mackenzie; Michael P Eastwood; Ron O Dror; David E Shaw
Journal:  J Chem Phys       Date:  2013-10-28       Impact factor: 3.488

6.  Canonical dynamics: Equilibrium phase-space distributions.

Authors: 
Journal:  Phys Rev A Gen Phys       Date:  1985-03

7.  Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature.

Authors:  O Berger; O Edholm; F Jähnig
Journal:  Biophys J       Date:  1997-05       Impact factor: 4.033

8.  Robust and efficient configurational molecular sampling via Langevin dynamics.

Authors:  Benedict Leimkuhler; Charles Matthews
Journal:  J Chem Phys       Date:  2013-05-07       Impact factor: 3.488

9.  MOIL-opt: Energy-Conserving Molecular Dynamics on a GPU/CPU system.

Authors:  A Peter Ruymgaart; Alfredo E Cardenas; Ron Elber
Journal:  J Chem Theory Comput       Date:  2011-08-26       Impact factor: 6.006

10.  Modeling kinetics and equilibrium of membranes with fields: milestoning analysis and implication to permeation.

Authors:  Alfredo E Cardenas; Ron Elber
Journal:  J Chem Phys       Date:  2014-08-07       Impact factor: 3.488

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Journal:  J Biol Chem       Date:  2020-02-17       Impact factor: 5.157

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Authors:  Rebika Shrestha; Cari M Anderson; Alfredo E Cardenas; Ron Elber; Lauren J Webb
Journal:  J Phys Chem B       Date:  2017-01-26       Impact factor: 2.991

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Journal:  Comput Struct Biotechnol J       Date:  2022-06-25       Impact factor: 6.155

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Journal:  ACS Omega       Date:  2022-04-21

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Authors:  Myungjin Lee; Anita Changela; Jason Gorman; Reda Rawi; Tatsiana Bylund; Cara W Chao; Bob C Lin; Mark K Louder; Adam S Olia; Baoshan Zhang; Nicole A Doria-Rose; Susan Zolla-Pazner; Lawrence Shapiro; Gwo-Yu Chuang; Peter D Kwong
Journal:  Nat Commun       Date:  2021-11-09       Impact factor: 14.919

7.  Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant.

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Journal:  Int J Mol Sci       Date:  2022-02-16       Impact factor: 5.923

8.  Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant.

Authors:  Gennady M Verkhivker; Steve Agajanian; Deniz Yasar Oztas; Grace Gupta
Journal:  ACS Omega       Date:  2021-06-09

9.  In Silico Screening of Potential Spike Glycoprotein Inhibitors of SARS-CoV-2 with Drug Repurposing Strategy.

Authors:  Tian-Zi Wei; Hao Wang; Xue-Qing Wu; Yi Lu; Sheng-Hui Guan; Feng-Quan Dong; Chen-le Dong; Gu-Li Zhu; Yu-Zhou Bao; Jian Zhang; Guan-Yu Wang; Hai-Ying Li
Journal:  Chin J Integr Med       Date:  2020-08-01       Impact factor: 1.978

10.  Coevolution, Dynamics and Allostery Conspire in Shaping Cooperative Binding and Signal Transmission of the SARS-CoV-2 Spike Protein with Human Angiotensin-Converting Enzyme 2.

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Journal:  Int J Mol Sci       Date:  2020-11-04       Impact factor: 5.923

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