Molecular Dynamics Simulations with NAMD2

Methods Mol Biol. 2019;2053:109-124. doi: 10.1007/978-1-4939-9752-7_8.


X-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 structure obtained from experimental techniques or generated using homology modeling. In this chapter, we describe in detail a tutorial to carry out molecular dynamics simulations using the program NAMD2. We chose as a molecular system to simulate the structure of human cyclin-dependent kinase 2.

Keywords: Cyclin-dependent kinase 2; Drug design; Force fields; Molecular dynamics; Molecular recognition; NAMD2.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphate / chemistry
  • Algorithms
  • Crystallography, X-Ray
  • Cyclin-Dependent Kinase 2 / chemistry
  • Humans
  • Molecular Dynamics Simulation*
  • Protein Conformation
  • Software*
  • Static Electricity
  • User-Computer Interface


  • Adenosine Triphosphate
  • CDK2 protein, human
  • Cyclin-Dependent Kinase 2