[PDF] Top 20 A test problem for molecular dynamics integrators
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A test problem for molecular dynamics integrators
... a test problem for evaluating the ability of time-stepping methods to preserve the statistical properties of systems in molecular ...numerical integrators, including the symplectic Euler ... See full document
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Molecular dynamics integration and molecular vibrational theory. I. New symplectic integrators
... high-frequency molecular vibrational motion uses also a shorter integration time step for the numerical integration of high-frequency anharmonic vibration terms and a correspondingly longer time step for the ... See full document
14
High-throughput of measure-preserving integrators for constant temperature molecular dynamics simulations on GPUs
... Abstract: Molecular dynamics simulation is currently the theoretical technique eligible to simulate a wide range of systems from soft condensed matter to biological ...of molecular dynamics in ... See full document
12
Some robust integrators for large time dynamics
... Originally, Dirac structures appear in the work of Courant [6]. The initial motivation was coming from mechanics. As is known, for mechanical systems one can choose between Lagrangian and Hamiltonian formalisms, both ... See full document
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TO THE PROBLEM OF FORMULATION OF BASIC PRINCIPLES IN THE THEORY OF MOLECULAR STRUCTURE AND DYNAMICS
... the molecular system consisting of 30 − 40 atomic objects the number of possible stable structures might be as large as hundreds of ...isomerization problem because the existence of multiple isomers is not ... See full document
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Variational integrators
... Some relevant statistics are collected in Table 6.2. Overall, in the present example the number of AVI updates is roughly 15% of the number of updates required by explicit Newmark at constant time step. It should be ... See full document
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Benchmark cases for robust explicit time integrators in non-smooth transient dynamics
... tact constraints but induce an implicit contact problem. Contact problems are divided into smooth and non-smooth ones. A smooth contact problem, like persistent contact, keeps the regularity of velocities, ... See full document
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Molecular Dynamics. r F. r dt. What is molecular dynamics?
... protein-folding problem is one of the major challenges of molecular ...folding problem in MD simulation one has to follow the evolution of a large molecule in a solution for at least ... See full document
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The effects of element shape on the critical time step in explicit time integrators for elasto-dynamics
... eigenvalue problem has been formulated and solved on element level for a number of cases, and the maximum eigenfrequencies have been identified in symbolic form making use of appropriate parameters to capture the ... See full document
16
Reweighting methods for Molecular Dynamics
... of molecular processes, the estimation of time-scales and transition rates, has become ...tween molecular conformations is – from a mathematical point of view – an invariant subspace projection ...of ... See full document
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Validation of molecular dynamics simulation
... We note that the different properties possess very differ- ent relaxation times, which means that MD simulations of very different lengths are required to obtain converged simu- lated values suitable for comparison to ... See full document
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Molecular dynamics pre-simulations for nanoscale computational fluid dynamics
... we test the robustness of our enhanced CFD technique for cases where, in some region of the flow field, the continuum-fluid assumption is far from being valid, and where there also exist large regions of bulk ... See full document
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Molecular dynamics pre simulations for nanoscale computational fluid dynamics
... we test the robustness of our enhanced CFD technique for cases where, in some region of the flow field, the continuum-fluid assumption is far from being valid, and where there also exist large regions of bulk ... See full document
15
Molecular dynamics simulation of amphiphilic aggregates
... contribution of the three terms depends on the convention used for the definition of the regions. We also performed computational tests with artificial molecules A1 and A2. After we performed our test runs we ... See full document
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mdFoam+ : advanced molecular dynamics in OpenFOAM
... mdFoam + provides an MPI based domain-decomposition method for performing parallel MD simulations. Generally the concept is that the mesh, which represents the entire domain to be simulated, is first split up, or ... See full document
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Superadiabatic transitions in quantum molecular dynamics
... the problem (see below), it is known [1, 5] that there exists an optimal superadiabatic representation in which transitions are (uniformly in time) exponentially small, and have the universal shape of an error ... See full document
26
Molecular Dynamics Simulation of Protein Biosurfactants
... and function [91,134]. Despite the success of MD simulation, they face a number of limitations. Possibly the largest outstanding question is the transferability of models used for protein simulations to interfacial and ... See full document
19
Jovian Problem: Performance of Some High Order Numerical Integrators
... Let us now consider the accuracy of the integrators in terms of the relative error in energy and angular momen- tum. Figure 4 shows the error growth in the energy for the Jovian problem. The integration has ... See full document
10
Visualizing Molecular Dynamics
... Initialize atomic coordinates, velocities, accelerations & step count before entering the GLUT main loop in main(). InitParams(); // Read and initialize MD parameters InitConf();[r] ... See full document
16
Molecular Dynamics Simulations
... • Force fields are constructed by parameterising the potential functions using either experimental data (X- ray and electron diffraction, NMR and IR spectroscopy) or ab initio and semi-e[r] ... See full document
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