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Simulation report

Technical information

General information

Name: smoothened homolog (apoform) (apoform)

PDB id: 4JKV

Activation state: Inactive

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 (156 mM), Chloride (161 mM)

Number of molecules:

Water: 22755

POPC: 188

Chloride: 66

Sodium ion: 64

Smoothened homolog: 1

Total number of atoms: 99409

Simulation details

Software and version: ACEMD3, GPUGRID

Forcefield and version: CHARMM, c36 Jul 2020

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"

Simulation components

Receptor

PDB id: 4JKV
Smoothened homolog

Visualization and trajectory sharing powered by NGL viewer and MDSrv

Open with GPCRmd Workbench

Mutations

No mutations found



Other molecules



POPC

Specific State ID: 5152

(188 molecules)


Sodium ion

Specific State ID: 5153

(64 molecules)

Na+


Chloride

Specific State ID: 5154

(66 molecules)

Cl-


Water

Specific State ID: 5151

(22755 molecules)

H2O


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