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Simulation report

Technical information

General information

Name: Partially thermostabilized beta-1 adrenergic receptor (apoform)

PDB id: 2YCW.A

Activation state: Inactive

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 (159 mM), Chloride (200 mM)

Number of molecules:

Water: 16086

POPC: 169

Chloride: 58

Sodium ion: 46

Beta-1 adrenergic receptor: 1

Total number of atoms: 75879

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"


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


Visualization and trajectory sharing powered by NGL viewer and MDSrv

Open with GPCRmd Workbench


Table of simulated mutations

(Mutations shown in blue at the viewer)

Residue ID Residue seq. position Generic num. From To
227 227 5x58 Y A
282 282 6x27 A L

Other molecules

Sodium ion

Specific State ID: 5016

(46 molecules)



Specific State ID: 5017

(58 molecules)



Specific State ID: 5018

(169 molecules)


Specific State ID: 5019

(16086 molecules)