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.
Citations
More filters
TL;DR: This analysis highlights the presence of the asymptotic power law decay of the waiting time probability density of the stochastic process involved, thereby illustrating the connection between approaches based on fractional diffusion equations and the continuous time random walk.
Abstract: In this article, we investigate the multiple-scale structure of methyl side chain dynamics in proteins. We show that the orientational correlation functions of CH3 methyl groups are well described by a fractional Brownian dynamics model. Typical angular correlation functions involved in NMR relaxation were computed from MD simulations performed on two different proteins. These correlation functions were shown to be very well fitted by a fractional Ornstein–Uhlenbeck process in the presence of effective local potentials at the C–H and C–C methyl bonds. In addition, our analysis highlights the presence of the asymptotic power law decay of the waiting time probability density of the stochastic process involved, thereby illustrating the connection between approaches based on fractional diffusion equations and the continuous time random walk.
7 citations
TL;DR: In this paper, the structure and vibrational properties of water molecules confined in unidirectional hydrophilic nanopores of AlPO4-54•xH2O were investigated from room temperature down to 10 K by single crystal synchrotron X-ray diffraction, neutron pair distribution function analysis, incoherent inelastic neutron scattering, farand mid-infrared spectroscopy, ab-initio molecular dynamics and Grand Canonical Monte Carlo Simulations.
Abstract: The structure and vibrational properties of water molecules confined in unidirectional hydrophilic nanopores of AlPO4-54•xH2O were investigated from room temperature down to 10 K by single crystal synchrotron X-ray diffraction, neutron pair distribution function analysis, incoherent inelastic neutron scattering, farand mid-infrared spectroscopy, ab-initio Molecular Dynamics and Grand Canonical Monte Carlo Simulations. The ensemble of results indicates that water confined in AlPO4-54•xH2O nanopores does not crystallize down to 10 K and points at the existence of two different types of water networks, whose local arrangement and dynamical behavior become more and more distinguished when lowering the temperature below 150 K. The dependence of temperature of the infrared spectroscopy points at two transitions at 250 and 150 K. Upon cooling, water close to the zeolite pore wall shows a highly ordered local arrangement induced by the pore wall, with more defined site occupancy and lower density with respect to bulk water. Conversely, water in the pore core shows a denser, more disordered and orientationally distorted arrangement, and a glassy-like behavior down to the lowest investigated temperature.
6 citations
TL;DR: In this article, the effects of several key variables on the dimensions and the dynamics of Intrinsically Disordered Proteins (IDP) were investigated using coarse-grained polymer models informed by experimental observations.
Abstract: Unlike the well defined structures of classical natively folded proteins, Intrinsically Disordered Proteins (IDP) and Intrinsically Disordered Regions (IDR) dynamically span large conformational and structural ensembles. This dynamic disorder impedes the study of the relationship between the amino acid sequences of the IDPs and their spatial structures, dynamics and function. Multiple experimental and theoretical evidence points in many cases to the overall importance of the general properties of the amino acid sequence of the IPDs rather than their precise atomistic details. However, while different experimental techniques can probe aspects of the IDP conformations, often different techniques or conditions offer seemingly contradictory results. Using coarse-grained polymer models informed by experimental observations, we investigate the effects of several key variables on the dimensions and the dynamics of IDPs. The coarse-grained simulations are in a good agreement with the results of atomistic MD. We show that the sequence composition and patterning are well reflected in the global conformational variables such as the radius of gyration and hydrodynamic radius, while the end-to-end distance and dynamics are highly sequence specific. We identify the conditions that allow mapping of highly heterogeneous sequences of IDPs onto averaged minimal polymer models. We discuss the implications of these results for the interpretation of the recent experimental measurements, and for further development of appropriate mesoscopic models of IDPs.
6 citations
TL;DR: In this article, the equivalence or differences between classical force fields with rigid bond lengths and the same models but with (harmonic) bond length potentials were investigated, and a range of values for the force constant of the bond-length potentials (expressed in terms of the period-length of bond-oscillations) were obtained.
Abstract: This study investigates the equivalence or differences between classical force fields with rigid bond lengths and the same models but with (harmonic) bond length potentials. For ethane, propane, and dimethyl ether described with the Transferable Anisotropic Mie potential, we vary the force constant of the harmonic bond length potentials and analyze static and dynamic physical properties, namely pressure, viscosity, self-diffusion, and thermal conductivity of homogeneous phases. We find a range of values for the force constant of the bond length potentials (expressed in terms of the period-length of bond-oscillations) where force fields with harmonic bond lengths give equivalent results as the model with rigid bond lengths for static properties, for viscosity, and for self-diffusion coefficients. The thermal conductivity of the force field with rigid bond lengths has an offset compared to the harmonic bond length models, which can be approximated through an analytic correction term. After adding the correc...
5 citations
References
More filters
TL;DR: In this article, a modified Monte Carlo integration over configuration space is used to investigate the properties of a two-dimensional rigid-sphere system with a set of interacting individual molecules, and the results are compared to free volume equations of state and a four-term virial coefficient expansion.
Abstract: A general method, suitable for fast computing machines, for investigating such properties as equations of state for substances consisting of interacting individual molecules is described. The method consists of a modified Monte Carlo integration over configuration space. Results for the two‐dimensional rigid‐sphere system have been obtained on the Los Alamos MANIAC and are presented here. These results are compared to the free volume equation of state and to a four‐term virial coefficient expansion.
35,161 citations
"nMoldyn - Interfacing spectroscopic..." refers background in this paper
...[1] to study the equation of state of model liquids and the pioneering molecular dynamics (MD) study of liquid argon by Rahman, which extended the scope of computer simulations to time dependent phenomena [2]....
[...]
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
34,239 citations
"nMoldyn - Interfacing spectroscopic..." refers methods in this paper
...The lysozyme structure was taken from the Brookhaven protein data bank [28] (code 193L[29]) and hydrogen atoms were added to the structure according to standard criteria concerning the chemical bond structure of amino acids....
[...]
TL;DR: An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms.
Abstract: An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms. Timings and accuracies are presented for three large crystalline ionic systems.
24,332 citations
"nMoldyn - Interfacing spectroscopic..." refers methods in this paper
...To mimic a macroscopic system, periodic boundary conditions have been applied and electrostatic interactions have been computed using the particle mesh Ewald method (PME) [53], with a cut-off of 12 Å....
[...]
Book•
01 Jan 1986
TL;DR: In this paper, the authors propose a recursive least square adaptive filter (RLF) based on the Kalman filter, which is used as the unifying base for RLS Filters.
Abstract: Background and Overview. 1. Stochastic Processes and Models. 2. Wiener Filters. 3. Linear Prediction. 4. Method of Steepest Descent. 5. Least-Mean-Square Adaptive Filters. 6. Normalized Least-Mean-Square Adaptive Filters. 7. Transform-Domain and Sub-Band Adaptive Filters. 8. Method of Least Squares. 9. Recursive Least-Square Adaptive Filters. 10. Kalman Filters as the Unifying Bases for RLS Filters. 11. Square-Root Adaptive Filters. 12. Order-Recursive Adaptive Filters. 13. Finite-Precision Effects. 14. Tracking of Time-Varying Systems. 15. Adaptive Filters Using Infinite-Duration Impulse Response Structures. 16. Blind Deconvolution. 17. Back-Propagation Learning. Epilogue. Appendix A. Complex Variables. Appendix B. Differentiation with Respect to a Vector. Appendix C. Method of Lagrange Multipliers. Appendix D. Estimation Theory. Appendix E. Eigenanalysis. Appendix F. Rotations and Reflections. Appendix G. Complex Wishart Distribution. Glossary. Abbreviations. Principal Symbols. Bibliography. Index.
16,062 citations
"nMoldyn - Interfacing spectroscopic..." refers methods in this paper
...one obtains finally an approximation for the Fourier spectrum of the ACF of a(t), which is based on the AR model [61, 64],...
[...]
TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.
Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.
14,558 citations
"nMoldyn - Interfacing spectroscopic..." refers methods in this paper
...The MD trajectory used for the calculation nMoldyn has been computed by the program package NAMD [51]....
[...]