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Molecular dynamics simulations in biology
Nature, 1990Molecular dynamics--the science of simulating the motions of a system of particles--applied to biological macromolecules gives the fluctuations in the relative positions of the atoms in a protein or in DNA as a function of time. Knowledge of these motions provides insights into biological phenomena such as the role of flexibility in ligand binding and ...
M, Karplus, G A, Petsko
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Fluctuations in molecular dynamics simulations
Mathematics and Computers in Simulation, 2010zbMATH Open Web Interface contents unavailable due to conflicting licenses.
J. J. Hoyt, Z. T. Trautt, M. Upmanyu
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Computing in Science & Engineering, 1999
The article presents a discussion on molecular dynamics (MD) simulation. MD requires a description of the molecules and the forces that act between them; a well known example is the Lennard-Jones potential, in which spherical particles repel one another at close range but otherwise attract.
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The article presents a discussion on molecular dynamics (MD) simulation. MD requires a description of the molecules and the forces that act between them; a well known example is the Lennard-Jones potential, in which spherical particles repel one another at close range but otherwise attract.
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Molecular Dynamics Simulation of Proteins
2019Molecular dynamics simulations allow the conformational motion of a molecule such as a protein to be followed over time at atomic-level detail. Several choices need to be made prior to running a simulation, including the software, which molecules to include in the simulation, and the force field used to describe their behavior. Guidance on making these
Thomas A, Collier +2 more
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Reconfigurable Molecular Dynamics Simulator
12th Annual IEEE Symposium on Field-Programmable Custom Computing Machines, 2004Current high-performance applications are typically implemented on large-scale general-purpose distributed or multiprocessing systems often based on commodity microprocessors. Field-Programmable Gate Arrays (FPGAs) have now reached a level of sophistication that they too could be used for such applications.
Navid Azizi +4 more
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Molecular Dynamics Simulation of Nanoindentation
2004Molecular dynamics simulations are used to investigate the nucleation and dynamics of dislocations during nanoindentation of a (111) FCC plane. The core structure around the dislocation is visualized by coloring the atoms with deviating coordination number and its Burgers vector is automatically determined.
Michielsen, K +3 more
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Molecular Dynamics Simulations of CYP2E1
Medicinal Chemistry, 2012CYP2E1, as a member of the cytochrome P450s (CYPs) super-family, is in charge of six percent drug metabolism involving a diversity of drugs distinct in structures and chemical properties, such as alcohols, monocyclic compounds (e.g., acetaminophen, benzene, p-nitrophenol), bicyclic heterocycles (e.g., coumarin, caffeine) and even fatty acids.
Jue, Li +4 more
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Molecular-dynamics simulations of sputtering
Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences, 2003The use of molecular-dynamics simulations to understand the ejection processes of particles from surfaces after energetic ion bombardment is discussed. Substrates considered include metals, covalent and ionic materials, polymers and molecular solids. It is shown how the simulations can be used to aid interpretation of experimental results by providing ...
Roger, Smith +2 more
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Molecular Dynamics Simulations
2008Molecular simulation is a very powerful toolbox in modern molecular modeling, and enables us to follow and understand structure and dynamics with extreme detail--literally on scales where motion of individual atoms can be tracked. This chapter focuses on the two most commonly used methods, namely, energy minimization and molecular dynamics, that ...
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Molecular Dynamics Simulations with NAMD2
2019X-ray diffraction crystallography is the primary technique to determine the three-dimensional structures of biomolecules. Although a robust method, X-ray crystallography is not able to access the dynamical behavior of macromolecules. To do so, we have to carry out molecular dynamics simulations taking as an initial system the three-dimensional ...
Gabriela, Bitencourt-Ferreira +1 more
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