Simulation report
Technical information
General information
Name: Rhodopsin in complex with lysine-retinol
PDB id: 3C9M
Activation state: Inactive
Description: Classical unbiased (NVT ensemble) complex flexibility assay.
Submitted by: GPCRmd community
System setup
Solvent type: TIP3P
Membrane type: Homogeneous
Membrane composition: POPC
Ionic composition: Sodium ion (159 mM), Chloride (170 mM)
Number of molecules:
Water: 14369
POPC: 171
Chloride: 44
Sodium ion: 41
N~6~-[(2z,4e,6e,8e)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenyl]lysine: 1
Rhodopsin: 1
Total number of atoms: 71343
Simulation details
Software and version: ACEMD3, GPUGRID
Forcefield and version: CHARMM, c36 Jul 2020
Time step : 4.0 fs
Delta : 0.2 ns
Replicates: 3
Accumulated simulation time: 1.5 µs
Additonal parameters: Available at "Simulation protocol & starting files"
Simulation components
Ligands
N~6~-[(2z,4e,6e,8e)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenyl]lysine
(1 molecule)
Receptor
Mutations
No mutations found
Other molecules
N~6~-[(2z,4e,6e,8e)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenyl]lysine (orthosteric lig.)
Specific State ID: 5282(1 molecule)