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Effect of different treatments of long‐range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer
Author(s) -
Cordomí Arnau,
Edholm Olle,
Perez Juan J.
Publication year - 2007
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20579
Subject(s) - molecular dynamics , rhodopsin , chemistry , lipid bilayer , electrostatics , chemical physics , work (physics) , cutoff , bilayer , sampling (signal processing) , range (aeronautics) , ewald summation , umbrella sampling , statistical physics , biological system , thermodynamics , computational chemistry , physics , materials science , membrane , optics , biochemistry , quantum mechanics , detector , biology , composite material , retinal
The present study analyzes the effect of the simulation conditions on the results of molecular dynamics simulations of G‐protein coupled receptors (GPCRs) performed with an explicit lipid bilayer. Accordingly, the present work reports the analysis of different simulations of bovine rhodopsin embedded in a dipalmitoyl phosphatidylcholine (DPPC) lipid bilayer using two different sampling conditions and two different approaches for the treatment of long‐range electrostatic interactions. Specifically, sampling was carried out either by using the statistical ensembles NVT or NPT (constant number of atoms, a pressure of 1 atm in all directions and fixed temperature), and the electrostatic interactions were treated either by using a twin‐cutoff, or the particle mesh Ewald summation method (PME). The results of the present study suggest that the use of the NPT ensemble in combination with the PME method provide more realistic simulations. The use of NPT during the equilibration avoids the need of an a priori estimation of the box dimensions, giving the correct area per lipid. However, once the system is equilibrated, the simulations are irrespective of the sampling conditions used. The use of an electrostatic cutoff induces artifacts on both lipid thickness and the ion distribution, but has no direct effect on the protein and water molecules. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007