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: In this paper , a comparison of transferable force fields for the prediction of different thermophysical properties of alkanes at extreme conditions, as they are encountered in tribological applications, was carried out using molecular dynamics simulations.
Abstract: The prediction of thermophysical properties at extreme conditions is an important application of molecular simulations. The quality of these predictions primarily depends on the quality of the employed force field. In this work, a systematic comparison of classical transferable force fields for the prediction of different thermophysical properties of alkanes at extreme conditions, as they are encountered in tribological applications, was carried out using molecular dynamics simulations. Nine transferable force fields from three different classes were considered (all-atom, united-atom, and coarse-grained force fields). Three linear alkanes (n-decane, n-icosane, and n-triacontane) and two branched alkanes (1-decene trimer and squalane) were studied. Simulations were carried out in a pressure range between 0.1 and 400 MPa at 373.15 K. For each state point, density, viscosity, and self-diffusion coefficient were sampled, and the results were compared to experimental data. The Potoff force field yielded the best results.
3 citations
TL;DR: In this paper , the interplay between organization and dynamics in bulk liquid acetonitrile was examined using angularly resolved radial distribution functions derived from molecular simulations, and the authors identified a complex microscopic structure in which most liquid molecules are associated with one or more neighboring molecules in an antiparallel, octupole-paired configuration and/or an offset, head-to-tail configuration.
3 citations
TL;DR: In this article, the dynamics of bidisperse polymer melts using molecular dynamics and a bead-spring chain model were explored, and it was shown that adding short chains can significantly accelerate the long chains by substantially lessening their extent of entanglement.
Abstract: Polydispersity is inevitable in industrially produced polymers. Established theories of polymer dynamics and rheology, however, were mostly built on monodisperse linear polymers. Dynamics of polydisperse polymers is yet to be fully explored—specifically how chains of different lengths affect the dynamics of one another in a mixture. This study explored the dynamics of bidisperse polymer melts using molecular dynamics and a bead–spring chain model. Binary mixtures between a moderately entangled long-chain species and an unentangled or marginally entangled short-chain species were investigated. We found that adding short chains can significantly accelerate the dynamics of the long chains by substantially lessening their extent of entanglement. Meanwhile, although introducing long chains also hinders the motion of the short chains, it does not qualitatively alter the nature of their dynamics—unentangled short chains still follow classical Rouse dynamics even in a matrix containing entangled chains. Detailed Rouse mode analysis was used to reveal the effects of entanglement at chain segments of different scales. Stress relaxation following a step shear strain was also studied, and semi-empirical mixing rules that predict the linear viscoelasticity of polydisperse polymers based on that of monodisperse systems were evaluated with simulation results.
2 citations
TL;DR: In this paper , the effects of several key variables on the dimensions and the dynamics of IDPs using coarse-grained polymer models were investigated, and it was shown that in good solvent conditions highly heterogeneous sequences of IDP can be well mapped onto averaged minimal polymer models for the purpose of prediction of the IDPs dimensions and dynamic relaxation times.
Abstract: Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) perform diverse functions in cellular organization, transport and signaling. Unlike the well-defined structures of the classical natively folded proteins, IDPs and IDRs 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 and dynamics, with different experimental techniques often offering seemingly contradictory results. Although experimental and theoretical evidence indicates that some IDP properties can be understood based on their average biophysical properties and amino acid composition, other aspects of IDP function are dictated by the specifics of the amino acid sequence. We investigate the effects of several key variables on the dimensions and the dynamics of IDPs using coarse-grained polymer models. We focus on the sequence “patchiness” informed by the sequence and biophysical properties of different classes of IDPs—and in particular FG nucleoporins of the nuclear pore complex (NPC). 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 find that in good solvent conditions highly heterogeneous sequences of IDPs can be well mapped onto averaged minimal polymer models for the purpose of prediction of the IDPs dimensions and dynamic relaxation times. The coarse-grained simulations are in a good agreement with the results of atomistic MD. We discuss the implications of these results for the interpretation of the recent experimental measurements, and for the further applications of mesoscopic models of FG nucleoporins and IDPs more broadly.
1 citations
TL;DR: In this paper , a set of coupled Volterra equations is obtained that relate the projected time correlation functions between all the variables of interest, leading to a very convenient yet efficient strategy to obtain any projected-time correlation function or contribution to the memory kernel entering a generalized Langevin equation.
Abstract: Starting from the orthogonal dynamics of any given set of variables with respect to the projection variable used to derive the Mori-Zwanzig equation, a set of coupled Volterra equations is obtained that relate the projected time correlation functions between all the variables of interest. This set of equations can be solved using standard numerical inversion methods for Volterra equations, leading to a very convenient yet efficient strategy to obtain any projected time correlation function or contribution to the memory kernel entering a generalized Langevin equation. Using this strategy, the memory kernel related to the diffusion of tagged particles in a bulk Lennard-Jones fluid is investigated up to the long-term regime to show that the repulsive-attractive cross-contribution to memory effects represents a small but non-zero contribution to the self-diffusion coefficient.
1 citations
References
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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]....
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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....
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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....
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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],...
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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]....
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