Simulation report

Technical information

General information

Name: Adenosine receptor a2a (apoform)

PDB id: 5G53.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 (182 mM)

Number of molecules:

Water: 21046

POPC: 227

Chloride: 69

Sodium ion: 59

Adenosine receptor A2a: 1

Total number of atoms: 98659

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: 5G53.A
Adenosine receptor A2a

Visualization and trajectory sharing powered by NGL viewer and MDSrv

Open with GPCRmd Workbench

Mutations

No mutations found



Other molecules



Sodium ion

Specific State ID: 5016

(59 molecules)

Na+


Chloride

Specific State ID: 5017

(69 molecules)

Cl-


POPC

Specific State ID: 5018

(227 molecules)


Water

Specific State ID: 5019

(21046 molecules)

H2O