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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


PDB id: 3C9M

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Open with GPCRmd Workbench


No mutations found

Other molecules


Specific State ID: 5152

(171 molecules)

Sodium ion

Specific State ID: 5153

(41 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)


Specific State ID: 5154

(44 molecules)



Specific State ID: 5151

(14369 molecules)