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Simulation report

Technical information

General information

Name: Beta-2 adrenergic receptor (apoform)

PDB id: 4LDO.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 (158 mM), Chloride (178 mM)

Number of molecules:

Water: 19337

POPC: 196

Chloride: 62

Sodium ion: 55

Beta-2 adrenergic receptor: 1

Total number of atoms: 89361

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)



GPCRmd publication page: 1469

Simulation components

Receptor

Visualization and trajectory sharing powered by NGL viewer and MDSrv

Open with GPCRmd Workbench

Mutations

No mutations found



Other molecules



Water

Specific State ID: 5019

(19337 molecules)

H2O


Sodium ion

Specific State ID: 5016

(55 molecules)

Na+


POPC

Specific State ID: 5018

(196 molecules)


Chloride

Specific State ID: 5017

(62 molecules)

Cl-


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