Practical Aspects of Molecular Dynamics Simulations

Part of the Scientific Computation book series (SCIENTCOMP)


In this chapter, we will introduce some practical aspects of molecular dynamics simulations, such as designing the constraints (e.g., SHAKE), periodic boundary conditions, spherical cutoffs, treatment of the long-range interactions (in particular, electrostatic interactions), and identifying the equilibrium states of the simulations.


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© Springer Nature Switzerland AG 2020

Authors and Affiliations

  1. 1.Computer EngineeringInternational Balkan UniversitySkopjeNorth Macedonia
  2. 2.Advanced Computing Research CenterUniversity of New York TiranaTiranaAlbania

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