nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions
01 Jan 2011-Vol. 12, pp 201-232
TL;DR: A synoptic view of the range of applications of the latest version of nMoldyn is presented, which includes new modules for a simulation-based interpretation of data from nuclear magnetic resonance spectroscopy, far infraredSpectroscopy and for protein secondary structure analysis.
Abstract: This article gives an introduction into the program nMoldyn, which has been originally conceived to support the interpretation of neutron scattering experiments on complex molecular systems by the calculation of appropriate time correlation functions from classical and quantum molecular dynamics simulations of corresponding model systems. Later the functionality has been extended to include more advanced time series analyses of molecular dynamics trajectories, in particular the calculation of memory functions, which play an essential role in the theory of time correlation functions. Here we present a synoptic view of the range of applications of the latest version of nMoldyn, which includes new modules for a simulation-based interpretation of data from nuclear magnetic resonance spectroscopy, far infrared spectroscopy and for protein secondary structure analysis.
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TL;DR: The parts of this book of most interest and value to the EMC engineer will be the chapters on Thermal Noise, Antennas, Propagation and Transmission Lines, and Reflection and Refraction.
Abstract: dix A. Even if you don’t choose to memorize them this system aids in reference and retreival of important formulas. The book was compiled from notes developed during eight years of teaching a graduate course on the subject and was used as a text. Thus it has been student tested. Appendix F contains a number of problems, grouped to be used on a chapter by chapter basis The problems are designed to illustrate practical applications of the text material. The parts of this book of most interest and value to the EMC engineer will be the chapters on Thermal Noise, Antennas, Propagation and Transmission Lines, and Reflection and Refraction. This is not to downpade the chapters on Statistics and Its Applications, Signal Processing and Detection, and Some System Characteristics which also contain much potentially useful materials. Additional plus values for the book include a list of 40 references, a table of symbols used throughout the book, and a subject index. Some readers may find the condensed type and close line spacing hard to read. It was apparently set up by typewriter using an elite type face with single line spacing. When reduced down to a 6 by 9 5 inch size page it is too crowded for easy reading. In spite of this shortcoming your reviewer recommends this book as a worthwhile reference in this field of interest.
413 citations
TL;DR: Nine years after the original publication of TRAVIS, some of the recent new functions and features are highlighted, which contribute to make trajectory analysis more efficient.
Abstract: TRAVIS (“Trajectory Analyzer and Visualizer”) is a program package for post-processing and analyzing trajectories from molecular dynamics and Monte Carlo simulations, mostly focused on molecular condensed phase systems. It is an open source free software licensed under the GNU GPL, is platform independent, and does not require any external libraries. Nine years after the original publication of TRAVIS, we highlight some of the recent new functions and features in this article. At the same time, we shortly present some of the underlying algorithms in TRAVIS, which contribute to make trajectory analysis more efficient. Some modern visualization techniques such as Sankey diagrams are also demonstrated. Many analysis functions are implemented, covering structural analyses, dynamical analyses, and functions for predicting vibrational spectra from molecular dynamics simulations. While some of the analyses are known since several decades, others are very recent. For example, TRAVIS has been used to compute the first ab initio predictions in the literature of bulk phase vibrational circular dichroism spectra, bulk phase Raman optical activity spectra, and bulk phase resonance Raman spectra within the last few years.
263 citations
TL;DR: The freud Python package provides the core tools for finding particle neighbors in periodic systems, and offers a uniform API to a wide variety of methods implemented using these tools, enabling analysis of a broader class of data ranging from biomolecular simulations to colloidal experiments.
114 citations
TL;DR: The dependence of single-particle diffusion coefficients on the size and shape of the simulation box in molecular dynamics simulations of fluids and lipid membranes is investigated and it is found that the diffusion coefficients of lipids and a carbon nanotube embedded in a lipid membrane diverge with the logarithm of the box width.
Abstract: We investigate the dependence of single-particle diffusion coefficients on the size and shape of the simulation box in molecular dynamics simulations of fluids and lipid membranes. We find that the diffusion coefficients of lipids and a carbon nanotube embedded in a lipid membrane diverge with the logarithm of the box width. For a neat Lennard-Jones fluid in flat rectangular boxes, diffusion becomes anisotropic, diverging logarithmically in all three directions with increasing box width. In elongated boxes, the diffusion coefficients normal to the long axis diverge linearly with the height-to-width ratio. For both lipid membranes and neat fluids, this behavior is predicted quantitatively by hydrodynamic theory. Mean-square displacements in the neat fluid exhibit intermediate regimes of anomalous diffusion, with t ln t and t3/2 components in flat and elongated boxes, respectively. For membranes, the large finite-size effects, and the apparent inability to determine a well-defined lipid diffusion coefficien...
67 citations
References
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TL;DR: In this article, the authors compared the canonical distribution in both momentum and coordinate space with three recently proposed constant temperature molecular dynamics methods by: (i) Nose (Mol. Phys., to be published); (ii) Hoover et al. [Phys. Rev. Lett. 77, 63 (1983); and (iii) Haile and Gupta [J. Chem. Phys. 79, 3067 (1983).
Abstract: Three recently proposed constant temperature molecular dynamics methods by: (i) Nose (Mol. Phys., to be published); (ii) Hoover et al. [Phys. Rev. Lett. 48, 1818 (1982)], and Evans and Morriss [Chem. Phys. 77, 63 (1983)]; and (iii) Haile and Gupta [J. Chem. Phys. 79, 3067 (1983)] are examined analytically via calculating the equilibrium distribution functions and comparing them with that of the canonical ensemble. Except for effects due to momentum and angular momentum conservation, method (1) yields the rigorous canonical distribution in both momentum and coordinate space. Method (2) can be made rigorous in coordinate space, and can be derived from method (1) by imposing a specific constraint. Method (3) is not rigorous and gives a deviation of order N−1/2 from the canonical distribution (N the number of particles). The results for the constant temperature–constant pressure ensemble are similar to the canonical ensemble case.
13,921 citations
"nMoldyn - Interfacing spectroscopic..." refers methods in this paper
...A thermodynamic NpT -ensemble [30, 31], with T = 300K and p = 1atm was used....
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...To mimic realistic thermodynamic conditions the system was simulated in the thermodynamics NpT -ensemble, employing the extended system method [30, 31] with an integration time step of 0....
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Book•
01 Jan 1965
TL;DR: This chapter discusses the concept of a Random Variable, the meaning of Probability, and the axioms of probability in terms of Markov Chains and Queueing Theory.
Abstract: Part 1 Probability and Random Variables 1 The Meaning of Probability 2 The Axioms of Probability 3 Repeated Trials 4 The Concept of a Random Variable 5 Functions of One Random Variable 6 Two Random Variables 7 Sequences of Random Variables 8 Statistics Part 2 Stochastic Processes 9 General Concepts 10 Random Walk and Other Applications 11 Spectral Representation 12 Spectral Estimation 13 Mean Square Estimation 14 Entropy 15 Markov Chains 16 Markov Processes and Queueing Theory
13,886 citations
TL;DR: Weiner et al. as mentioned in this paper derived a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases.
Abstract: We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases. This effective two-body force field is the successor to the Weiner et al. force field and was developed with some of the same philosophies, such as the use of a simple diagonal potential function and electrostatic potential fit atom centered charges. The need for a 10-12 function for representing hydrogen bonds is no longer necessary due to the improved performance of the new charge model and new van der Waals parameters. These new charges are determined using a 6-31G* basis set and restrained electrostatic potential (RESP) fitting and have been shown to reproduce interaction energies, free energies of solvation, and conformational energies of simple small molecules to a good degree of accuracy. Furthermore, the new RESP charges exhibit less variability as a function of the molecular conformation used in the charge determination. The new van der Waals parameters have been derived from liquid simulations and include hydrogen parameters which take into account the effects of any geminal electronegative atoms. The bonded parameters developed by Weiner et al. were modified as necessary to reproduce experimental vibrational frequencies and structures. Most of the simple dihedral parameters have been retained from Weiner et al., but a complex set of 4 and yj parameters which do a good job of reproducing the energies of the low-energy conformations of glycyl and alanyl dipeptides has been developed for the peptide backbone.
12,660 citations
Book•
01 Jan 2002
TL;DR: In this paper, the meaning of probability and random variables are discussed, as well as the axioms of probability, and the concept of a random variable and repeated trials are discussed.
Abstract: Part 1 Probability and Random Variables 1 The Meaning of Probability 2 The Axioms of Probability 3 Repeated Trials 4 The Concept of a Random Variable 5 Functions of One Random Variable 6 Two Random Variables 7 Sequences of Random Variables 8 Statistics Part 2 Stochastic Processes 9 General Concepts 10 Random Walk and Other Applications 11 Spectral Representation 12 Spectral Estimation 13 Mean Square Estimation 14 Entropy 15 Markov Chains 16 Markov Processes and Queueing Theory
12,407 citations