Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs

Katsufumi Tomobe, Eiji Yamamoto, Kenji Yasuoka

Research output: Chapter in Book/Report/Conference proceedingChapter


Rhodopsin is a light-driven G protein-coupled receptor mediating signal transduction in eyes. The molecular dynamics (MD) simulations are powerful computational tools to investigate molecular behavior of proteins and internal water molecules which are related to the function of proteins; however, the MD simulations of the rhodopsin require several technical setups for accurate calculations. This chapter discusses practical methods for setting up the MD simulations of the rhodopsin [preparation of initial systems, condition files for MD simulation package GROMACS, and data analysis]. The data analysis includes the root mean square deviation (RMSD) and mapping of accessibility of water molecules.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages10
Publication statusPublished - 2019 Jan 1

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Biological membrane
  • G Protein-coupled receptor
  • Molecular dynamics simulations
  • Rhodopsin
  • Water pathway

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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