Simulation report

Technical information

General information

Name: G-protein coupled receptor homolog us28 (apoform)

PDB id: 4XT1.A

Activation state: Active

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 (157 mM), Chloride (167 mM)

Number of molecules:

Water: 16940

POPC: 154

Chloride: 51

Sodium ion: 48

G-protein coupled receptor homolog US28: 1

Total number of atoms: 76461

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

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

(48 molecules)

Na+


Chloride

Specific State ID: 5017

(51 molecules)

Cl-


POPC

Specific State ID: 5018

(154 molecules)


Water

Specific State ID: 5019

(16940 molecules)

H2O