How to Run FAST Simulations

M. I. Zimmerman, G. R. Bowman

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

8 Scopus citations


Molecular dynamics (MD) simulations are a powerful tool for understanding enzymes’ structures and functions with full atomistic detail. These physics-based simulations model the dynamics of a protein in solution and store snapshots of its atomic coordinates at discrete time intervals. Analysis of the snapshots from these trajectories provides thermodynamic and kinetic properties such as conformational free energies, binding free energies, and transition times. Unfortunately, simulating biologically relevant timescales with brute force MD simulations requires enormous computing resources. In this chapter we detail a goal-oriented sampling algorithm, called fluctuation amplification of specific traits, that quickly generates pertinent thermodynamic and kinetic information by using an iterative series of short MD simulations to explore the vast depths of conformational space.

Original languageEnglish
Title of host publicationMethods in Enzymology
PublisherAcademic Press Inc.
Number of pages13
StatePublished - 2016

Publication series

NameMethods in Enzymology
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988


  • Adaptive sampling
  • Allostery
  • Conformational change
  • Cryptic site
  • Goal-oriented sampling
  • Markov state model
  • Molecular dynamics simulations


Dive into the research topics of 'How to Run FAST Simulations'. Together they form a unique fingerprint.

Cite this