Minimization and Molecular Dynamics

Chapter

Abstract

For refinement of the receptor model on the one hand and to analyze conformational changes of the receptor on time scale on the other hand, in general molecular dynamic simulations of the receptor in its natural environment are performed. As a first step the so called setup of the simulation box is explained in detail and deals with the construction of the ligand, the receptor and the surrounding membrane. As the next step the embedding of the ligand-receptor complex into the membrane is elaborated with the help of appropriate LINUX commands. Finally different simulation protocols splitting the molecular dynamic procedure into a equilibration and a productive phase are presented.

Keywords

Molecular Dynamic Simulation Lipid Bilayer Force Constant Backbone Atom Receptor Model 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  1. 1.Institute of Pharmacy, Dept. of Pharm./Med. ChemistryUniversity of RegensburgRegensburgGermany
  2. 2.Faculty of Chemistry and PharmacyUniversity of RegensburgRegensburgGermany

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