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Get started in four steps

Get your first MD simulation running with your customized settings and parameters.

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Step 1: Submit your molecular and simulation files

In order to upload your files, you will first need to request a secure upload URL from us. This URL will give you temporary access to make an upload and has a TTL of 60 minutes.Through this URL, you will be able to submit molecular data (e.g., .pdb, .sdf) and custom force field files (e.g., .xml).
Once your file has been successfully uploaded through the secure upload-url, you’ll need to register that file with your account to begin using it in your MD simulations. Here, you’ll use the file_id obtained from the previous step and assign your file a new name.
Your registered file shows up automatically in your account upon success.

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Step 2: Build your simulation box

Before we run an MD simulation, make sure to build the system you’d like to run with first. If you’ve already built your system before, feel free to skip this step.Select the molecules to include in the system. This includes any previously uploaded custom molecule files, or a PDB ID.Review the available parameters for customization during the system build. These include force fields, water models, membrane embeddings, and more!
Now, let’s hit submit and wait just a few moments for your customized system to build!
  1. Your submitted system build will show up instantly in the System Board.
  2. Make sure to refresh your board periodically to get the latest status updates on your system build.
  3. See your system instantly, once it’s built, by viewing its Details.
  4. Make sure to refresh your System View periodically to ge the latest updates on your system build.
  5. Once the build has completed, you’ll now be able to submit MD simulations!
Check the simulation logs to see exactly what took place during the system build!

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Step 3: Submit your MD simulation

Once your system build has complete, you’ll now be able to start launching MD simulations.Select the system to simulate with via its system_id. Then, review the available parameters for customization during the system build.Finally, customize your simulation stages (e.g., energy minimization, equilibration, production), review your selections, and verify the price!
Now let’s hit submit and wait just a few moments for your MD simulation to begin!
  1. Your submitted simulation will show up instantly in the Job Board.
  2. Make sure to refresh your board periodically to get the latest status updates on your simulation.
  3. See your simulation results instantly, as it progresses, by viewing its Details.
  4. Make sure to refresh your Simulation View periodically to ge the latest updates on your simulation.
  5. Once the simulation has completed, you’ll now be able to perform analysis on the resulting trajectory!

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Step 4: Run your analysis

Once your simulation is complete, you can analyze the trajectory to understand its exact molecular interactions.Use Amber masking syntax to select residues, atoms, or chains and run analyses tailored to your needs.

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Step 5: Download your results

At any point once your simulation has completed, you can download the full set of simulation results in a zipped output bundle.This bundle will contain all intermediate structures and trajectories, as well as the final simulated production trajectory at full fidelity. All logs, including warnings and error outputs, are included in the bundle. You can use these outputs to simply visualize the simulation or even apply your own custom trajectory analysis!