Simulation report
Technical information
General information
Name: Active conformation of gpcr opsin stabilized by octylglucoside (apoform)
PDB id: 4J4Q
Activation state: Active
Description: Simulations generated using Adaptive sampling protocol. Each of the replicates corresponds to one stage of the simulation.
Submitted by: George Khelashvili, Weill Cornell Medical College
System setup
Solvent type: TIP3P
Membrane type: Heterogeneous
Membrane composition: POPG (9.1%), POPC (90.9%)
Ionic composition: Chloride (80 mM), Sodium ion (144 mM)
Number of molecules:
Water: 27006
POPC: 300
Sodium ion: 70
Chloride: 39
ZINC8437540: 30
Rhodopsin: 1
Total number of atoms: 130395
Simulation details
Software and version: ACEMD,
Forcefield and version: CHARMM, 36m Jul 2017
Time step : 2.0 fs
Delta : 1.6 ns
Replicates: 4
Accumulated simulation time: 51.608 µs
Additonal parameters: Available at "Simulation protocol & starting files"
References
Giulia Morra, Asghar M Razavi, Kalpana Pandey, Harel Weinstein, Anant K Menon, George Khelashvili. 2018. Mechanisms of Lipid Scrambling by the G Protein-Coupled Receptor Opsin. Structure 26 (2). doi: 10.1016/j.str.2017.11.020. (https://doi.org/10.1016/j.str.2017.11.020)
GPCRmd publication page: 1464
