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@@ -90,7 +90,7 @@ A few seconds after we will see an output similar to this:
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[lightdock3_setup] INFO: LightDock setup OK
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```
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**NOTE** For a detailed description of the setup stage, please check the [LightDock basics](https://lightdock.org/tutorials/0.9.2/basics#2-setup-a-simulation)
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**NOTE** For a detailed description of the setup stage, please check the [LightDock basics](https://lightdock.org/tutorials/0.9.3/basics#2-setup-a-simulation)
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{: .notice--warning}
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If the setup is successful, we will find a file called `setup.json`, which includes all the details about this LightDock simulation.
@@ -201,7 +201,7 @@ By default, and if no other scoring function is specified, LightDock makes use o
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As you may have noticed, we have instructed LightDock to use only 1 CPU core (`-c 1`). By default, LightDock will look for the total number of available cores. If you want to specify a different number, use the flag `-c`. MPI is also supported by using the `-mpi` flag.
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**NOTE** For more information about the simulation stage, please check the [LightDock basics](https://lightdock.org/tutorials/0.9.2./basics#3-run-a-simulation)
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**NOTE** For more information about the simulation stage, please check the [LightDock basics](https://lightdock.org/tutorials/0.9.3/basics#3-run-a-simulation)
Inside the `swarm_0` folder, we will find 200 new PDB structures corresponding to the 200 glowworm agents used in the current example. Try opening them on PyMOL and have a quick look at them:
**Congratulations!** You have successfully run your first docking simulation with LightDock!
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{: .notice--success}
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You can find all the simulation data already generated here: [simulation.tgz](/tutorials/0.9.2/simple_docking/data/simulation.tgz)
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You can find all the simulation data already generated here: [simulation.tgz](/tutorials/0.9.3/simple_docking/data/simulation.tgz)
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**Attention!** In this simple example we did not cluster predicted structures forthe different swarms (`swarm_0`in this case), but **for realistic simulations it is critical to always cluster intra-swarm structures**.
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