Structural and dynamical properties of manganese catalase and the synthetic protein DF1 and their implication for reactivity from classical molecular dynamics calculations

2006 ◽  
Vol 65 (2) ◽  
pp. 317-330 ◽  
Author(s):  
Katrin Spiegel ◽  
William F. De Grado ◽  
Michael L. Klein
Keyword(s):  
Molecular Dynamics ◽  
Manganese Catalase ◽  
Classical Molecular Dynamics ◽  
Synthetic Protein ◽  
Molecular Dynamics Calculations ◽  
Dynamical Properties

How to accurately model IR spectra of nanosized silicate grains

2019 ◽  
Vol 15 (S350) ◽  
pp. 431-433
Author(s):  
Joan Mariñoso Guiu ◽  
Antoni Macià ◽  
Stefan T. Bromley
Keyword(s):  
Molecular Dynamics ◽  
Ir Spectra ◽  
Density Functional ◽  
Effect Of Temperature ◽  
Chemical Compositions ◽  
Functional Theory ◽  
Classical Molecular Dynamics ◽  
Molecular Dynamics Calculations ◽  
Harmonic Oscillator Approximation ◽  
Dynamics Simulations

AbstractWe assess the accuracy of various computational methods for obtaining infrared (IR) spectra of nanosized silicate dust grains directly from their atomistic structure and atomic motions. First, IR spectra for a selection of small nanosilicate clusters with a range of sizes and chemical compositions are obtained within the harmonic oscillator approximation employing density functional theory (DFT) based quantum chemical calculations. To check if anharmonic effects play a significant role in the IR spectra of these nanoclusters, we further obtain their IR spectra from finite temperature DFT-based ab initio molecular dynamics (AIMD). Finally, we also study the effect of temperature on the broadening of the obtained IR spectra peaks in larger nanosilicate grains with a range of crystallinities. In this case, less computationally costly classical molecular dynamics simulations are necessary due to the large number of atoms involved. Generally, we find that although DFT-based methods are more accurate, surprisingly good IR spectra can also be obtained from classical molecular dynamics calculations.

scholarly journals Thermodynamic and dynamical properties of the hard sphere system revisited by molecular dynamics simulation

2019 ◽  
Vol 21 (13) ◽  
pp. 6886-6899 ◽  
Author(s):  
Sławomir Pieprzyk ◽  
Marcus N. Bannerman ◽  
Arkadiusz C. Brańka ◽  
Maciej Chudak ◽  
David M. Heyes
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Hard Sphere ◽  
Large System ◽  
Dynamics Simulation ◽  
Molecular Dynamics Calculations ◽  
Dynamical Properties ◽  
Number Of Particles

Revised thermodynamic and dynamical properties of the hard sphere (HS) system are obtained from extensive molecular dynamics calculations carried out with large system sizes (number of particles, N) and long times.

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