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Simulation report

Technical information

General information

Name: Apelin receptor in complex with single domain antibody jn241

PDB id: 6KNM

Description: Classical unbiased (NVT ensemble) complex flexibility assay.

Submitted by: Francho Nerín-Fonz, IMIM

System setup

Solvent type: Implicit

Membrane type: Homogeneous

Membrane composition: POPC

Ionic composition: Sodium ion (157 mM), Chloride (200 mM)

Number of molecules:

Water: 28626

POPC: 230

Chloride: 103

Sodium ion: 81

Apelin receptor: 1

Single domain antibody JN241: 1

Total number of atoms: 123845

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


Peptidic ligand(s)

Single domain antibody JN241

(1 molecule)


PDB id: 6KNM
Apelin receptor

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No mutations found

Other molecules


Specific State ID: 5152

(230 molecules)

Sodium ion

Specific State ID: 5153

(81 molecules)



Specific State ID: 5154

(103 molecules)



Specific State ID: 5151

(28626 molecules)