Simulation report
Technical information
General information
Name: Proteinase-activated receptor 1 in complex with vorapaxar
PDB id: 3VW7.A
Activation state: Intermediate
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: Chloride (182 mM), Sodium ion (161 mM)
Number of molecules:
Water: 13104
POPC: 154
Chloride: 43
Sodium ion: 38
Vorapaxar: 1
Proteinase-activated receptor 1: 1
Total number of atoms: 64843
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)
GPCRmd publication page: 1469
Simulation components
Ligands
Receptor
Mutations
No mutations found
