Simulation report

Technical information

General information

Name: Rhodopsin (apoform)

PDB id: 3PQR.A

Activation state: Active

Description: Classical unbiased (NVT ensemble) sodium allosteric binding assay.

Submitted by: GPCRmd community

System setup

Solvent type: TIP3P

Membrane type: Homogeneous

Membrane composition: POPC

Ionic composition: Sodium ion (156 mM), Chloride (168 mM)

Number of molecules:

Water: 14570

POPC: 161

Chloride: 44

Sodium ion: 41

Rhodopsin: 1

Total number of atoms: 70593

Simulation details

Software and version: ACEMD, GPUGRID

Forcefield and version: CHARMM, 36m Feb 2016

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"



References

Ismael Rodríguez-Espigares, Mariona Torrens-Fontanals, et al.. 2020. GPCRmd uncovers the dynamics of the 3D-GPCRome. Nature methods 17 (8). doi: 10.1038/s41592-020-0884-y. (http://doi.org/10.1038/s41592-020-0884-y)


Simulation components

Receptor

PDB id: 3PQR.A
Rhodopsin

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Mutations

No mutations found



Other molecules



Sodium ion

Specific State ID: 5016

(41 molecules)

Na+


Chloride

Specific State ID: 5017

(44 molecules)

Cl-


POPC

Specific State ID: 5018

(161 molecules)


Water

Specific State ID: 5019

(14570 molecules)

H2O