Published June 2025
| Version v1
Dataset
Open
P2Y1 purinergic receptor in the empty form 40 ns
Description
Classical MD simulations of the P2Y1 receptor in the empty form in the in the water-POPC bilayer. 0.15M of Na+ and Cl-. Three replicates are provided.
Trajectory originally donated to SlimMD
Files
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Files
(781.4 MB)
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md5:bfb4dd613e91ae7ce7da8fd52eb1f0d8
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252.4 MB | Download |
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md5:adc91be4d2f95c8b78392981758bc6da
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14.3 MB | Download |
Additional details
Identifiers
Domain Specific Metadata
| Property | Value |
|---|---|
| Software | NAMD |
| Software Version | Git-2017-12-19 |
| Molecular Model | atomistic |
| Simulation Method | classical |
| Timestep | 2 femtoseconds |
| Framestep | 0.2 nanoseconds |
| Length | 0.04 microseconds |
| Temperature | 310 K |
| Pressure | 1.01325 bar |
| Ensemble | NPT |
| Box Type | cubic |
| Trajectories | Cartesian coordinates |
| Force Fields | CHARMM36, CgenFF v1.0.0 |
| Experimental Structures | https://www.rcsb.org/structure/4XNW |
| Membrane | Yes |
| Ligands | N/A |
| Sequences | SFKCALTKTGFQFYYLPAVYILVFIIGFLGNSVAIWMFVFHMKPWSGISVYMFNLALADFLYVLTLPALIFYYFNKTDWIFGDAMCKLQRFIFHVNLYGSILFLTCISAHRYSGVVYPLKSLGRLKKKNAICISVLVWLIVVVAISPILFYSGTGVRKNKTITCYDTTSDEYLRSYFIYSMCTTVAMFCVPLVLILGCYGLIVRALIYKDLDNSPLRRKSIYLVIIVLTVFAVSYIPFHVMKTMNLRARLDFQTPAMCAFNDRVYATYQVTRGLASLNSCVDPILYFLAGDTFRRR |
| Box Dimensions | 80.2 x 73.3 x 170.7 Angstrom, alpha: 90.0, beta: 90.0, gamma: 90.0 degrees |
| Long Range Cutoff | 12 Angstrom |
| Thermostat | langevin |
| Barostat | langevin |
| Atom Count | 105179 |