Literature DB >> 15268177

Langevin dynamics in constant pressure extended systems.

D Quigley1, M I J Probert.   

Abstract

The advantages of performing Langevin dynamics in extended systems are discussed. A simple Langevin dynamics scheme for producing the canonical ensemble is reviewed, and is then extended to the Hoover ensemble. We show that the resulting equations of motion generate the isobaric-isothermal ensemble. The Parrinello-Rahman ensemble is then discussed and we show that despite the presence of intrinsic probability gradients in this system, a Langevin dynamics approach samples the extended phase space in the correct fashion. The implementation of these methods in the ab initio plane wave density functional theory code CASTEP [M. D. Segall, P. L. D. Lindan, M. J. Probert, C. J. Pickard, P. J. Hasnip, S. J. Clarke, and M. C. Payne, J. Phys.: Condens. Matter 14, 2717 (2003)] is demonstrated. (c) 2004 American Institute of Physics.

Year:  2004        PMID: 15268177     DOI: 10.1063/1.1755657

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  14 in total

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4.  Scalable molecular dynamics on CPU and GPU architectures with NAMD.

Authors:  James C Phillips; David J Hardy; Julio D C Maia; John E Stone; João V Ribeiro; Rafael C Bernardi; Ronak Buch; Giacomo Fiorin; Jérôme Hénin; Wei Jiang; Ryan McGreevy; Marcelo C R Melo; Brian K Radak; Robert D Skeel; Abhishek Singharoy; Yi Wang; Benoît Roux; Aleksei Aksimentiev; Zaida Luthey-Schulten; Laxmikant V Kalé; Klaus Schulten; Christophe Chipot; Emad Tajkhorshid
Journal:  J Chem Phys       Date:  2020-07-28       Impact factor: 3.488

5.  Structural, mechanistic, and physiological insights into phospholipase A-mediated membrane phospholipid degradation in Pseudomonas aeruginosa.

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Journal:  Elife       Date:  2022-05-10       Impact factor: 8.713

6.  Dynamics of metal binding and mutation in yybP-ykoY riboswitch of Lactococcus lactis.

Authors:  Mazhar Iqbal; Syed Tarique Moin
Journal:  RSC Adv       Date:  2022-06-13       Impact factor: 4.036

7.  A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation.

Authors:  Letizia Chiodo; Thérèse E Malliavin; Luca Maragliano; Grazia Cottone; Giovanni Ciccotti
Journal:  PLoS One       Date:  2015-07-24       Impact factor: 3.240

8.  Experimental and theoretical evidence of a supercritical-like transition in an organic semiconductor presenting colossal uniaxial negative thermal expansion.

Authors:  Arie van der Lee; Gilles H Roche; Guillaume Wantz; Joël J E Moreau; Olivier J Dautel; Jean-Sébastien Filhol
Journal:  Chem Sci       Date:  2018-03-22       Impact factor: 9.825

9.  Three-dimensional studies of pathogenic peptides from the c-terminal of Trypanosoma cruzi ribosomal P proteins and their interaction with a monoclonal antibody structural model.

Authors:  Osvaldo A Martín; Myriam E Villegas; Carlos F Aguilar
Journal:  PMC Biophys       Date:  2009-05-27

Review 10.  On flexible force fields for metal-organic frameworks: Recent developments and future prospects.

Authors:  Jurn Heinen; David Dubbeldam
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2018-03-25
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