Please find more detailed comments in jupyter notebook. Question: how to choose the best time step $\Delta t$ in MD? A brief Numerical analysis of $\Delta t$. Molecular dynamics simulations are an ...

1. Obtain Protein and GAG Structure for docking: In this tutorial, we will be docking a Heparan sulfate (HS) tetrasaccharide to human HS 3-O-sulfotransferase isoform 3 (3-OST-3), a key ...

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Molecular dynamics is a method that uses Newton’s equations of motion to computationally simulate the time evolution of a set of interacting atoms. Such techniques are dependent on a description of ...

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Fluid dynamics is the study of the motion of liquids, gases and plasmas. Flow is dependent on the intrinsic properties of the matter itself, such as compressibility, viscosity and density. Example ...

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