How Long Do MD Simulations Take? To ensure numerical stability, the time steps in an MD simulation must be short, typically only a few femtoseconds (10– 15 s) each. Most of the events of biochemical interest—for example, functionally important structural changes in proteins—take place on timescales of nanoseconds, microseconds, or longer. How would you go
What Is Atomistic Simulation? Atomistic simulations are a powerful tool for predicting dislocation-core structures on an atomic scale, but can suffer from serious artifacts, in particular depending on the determination of the interatomic potentials to which they are very sensitive. Why do we do MD simulation? Molecular dynamics (MD) is a computer simulation method for
What Is SPC E Water? The SPC/E model of Water was developed by Berendsen and coworkers [1]. It models Water as a rigid molecule containing three atomic centers, one Oxygen atom and two Hydrogen atoms. The Oxygen-Hydrogen bond length is fixed at 1Å and the Hydrogen-Oxygen-Hydrogen bond angle is fixed at 109.47°. What is SPC