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Journal ArticleDOI

nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions

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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Citations
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Alan R. Jones1

1,349 citations

01 Sep 1978
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

Journal ArticleDOI
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

Journal ArticleDOI
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

Journal ArticleDOI
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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Journal ArticleDOI
TL;DR: In this paper, the authors investigated the characteristics of low-frequency vibrations using the molecular dynamics method and calculated the density of states from the simulations and directly compared with the data derived from the experiments.
Abstract: The low‐frequency (<20 meV) polarized vibrational density of states in crystalline polyacetylene has recently been derived from inelastic neutron scattering data [J. L. Sauvajol, D. Djurado, A. J. Dianoux, N. Theophilou, and J. E. Fischer, Phys. Rev. B 43, 14 305 (1991)]. The spectral profiles were found to be highly anisotropic and to vary considerably with the chain conformation (cis or trans). Here we investigate the characteristics of the low‐frequency vibrations using the molecular dynamics method. Densities of states are calculated from the simulations and directly compared with the data derived from the experiments. The anisotropic and conformation‐dependent profiles are mostly well reproduced. The simulation trajectories are further analyzed so as to determine the dynamical contributions to the observed spectra. The lowest‐frequency vibrations parallel to the chain axes, at 1.5 meV in the cis system and 4 meV in the trans system, are found to result from whole‐molecule rigid‐body translations, invariant with chain length. Conversely, the low‐frequency intramolecular vibrations are weakly dependent on chain conformation but vary strongly with the chain length.

21 citations

01 Jan 2005
TL;DR: Coutsias et al. as discussed by the authors compared the Kabsch method and the quaternion method to find the optimal superposition of two molecular structures, which is based on a representation of rotations by quaternions.
Abstract: Coutsias et al. have recently published a method to find the optimal rotational superposition of two molecular structures, which is based on a representation of rotations by quaternions (J. Comp. Chem. 25(15), 1849 (2004)). The method, which has been suggested by other authors before, is compared to the one by Kabsch, where the elements of the rotation matrix are directly used as variables of the optimization problem. The statement that the two methods are equivalent is misleading in the sense that the Kabsch method may yield an improper optimal rotation, which must be explicitly checked for, whereas the quaternion method does not mix proper and improper rotations. Neverthe- less, both types of solutions can be considered by solving the same eigenvector problem. The relation between the two types of solutions is briefly discussed and bounds for the eigenvalues are given.

15 citations

Journal ArticleDOI
TL;DR: The results indicate that the design of new NA inhibitors should take into account these family-specific effects induced on the whole structure of NAs, and although NA1 and NA9 share almost the same oseltamivir-bound final conformation, they show some relevant differences as suggested by the ScrewFit algorithm.

14 citations

Journal ArticleDOI
TL;DR: The method to find the optimal rotational superposition of two molecular structures, which is based on a representation of rotations by quaternions, is compared to the one by Kabsch, where the elements of the rotation matrix are directly used as variables of the optimization problem.
Abstract: Coutsias et al. have recently published a method to find the optimal rotational superposition of two molecular structures, which is based on a representation of rotations by quaternions (J. Comp. Chem. 25(15), 1849 (2004)). The method, which has been suggested by other authors before, is compared to the one by Kabsch, where the elements of the rotation matrix are directly used as variables of the optimization problem. The statement that the two methods are equivalent is misleading in the sense that the Kabsch method may yield an improper optimal rotation, which must be explicitly checked for, whereas the quaternion method does not mix proper and improper rotations. Nevertheless, both types of solutions can be considered by solving the same eigenvector problem. The relation between the two types of solutions is briefly discussed and bounds for the eigenvalues are given.

13 citations


"nMoldyn - Interfacing spectroscopic..." refers methods in this paper

  • ...As demonstrated in previous works [32, 54], the...

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  • ...In order to extract a trajectory describing only the internal dynamics of the simulated lysozyme molecule, global translations and rotations of the protein molecule have been filtered out by performing for each sampling time step a rigid body fit of its actual conformation to its initial conformation in the trajectory [32, 54]....

    [...]

Journal ArticleDOI
TL;DR: In this paper, the low-frequency dynamics of pure and sodium-doped trans polyacetylene are investigated using a combination of incoherent neutron scattering spectroscopy and molecular dynamics simulations.
Abstract: The low‐frequency dynamics (<20 meV) of pure and sodium‐doped trans polyacetylene are investigated using a combination of incoherent neutron scattering spectroscopy and molecular dynamics simulations. The simulations are performed using a molecular mechanics potential function and including explicitly the three‐dimensional crystal environments of the molecules. Both the experiments and the simulations indicate that doping results in a marked change in the vibrational density of states of the polyene chains in the direction perpendicular to the chain axes, a broad minimum appearing at ∼16 meV. This spectral region is dominated by intramolecular torsional displacements. The results also suggest that the mean‐square displacements of the polyacetylene atoms become more isotropic on doping. The contributions of various rigid‐body motions to the simulation‐derived mean‐square displacements and vibrations are described.

11 citations