This tutorial will introduce you to a basic molecular dynamics simulation in Gromacs on Rescale. You will be shown step-by-step how to setup and submit a job from scratch, if you follow the directions contained in this document. Alternatively, you can click Import Job Setup in the top right of the page to clone the job that we have already run for you. You are free to modify any of the settings in the cloned job to become familiar with the Rescale platform.
Please contact us if you’re having trouble.
Visualization of a similar molecular dynamics simulation using DPPC membranes with an embedded protein. (Image courtesy of Justin Lemkul)
Description of the Simulation
Duration: Approximately 23 minutes. Alternatively, you can also click the Get Job Results link above, and review the full setup and results for the molecular dynamics simulation with Gromacs.
The Simulation: A phospholipid membrane, consisting of 1024 dipalmitoylphosphatidylcholine (DPPC) lipids in a bilayer configuration with 23 water molecules per lipid, for a total of 121,856 atoms.
The Workflow: This tutorial will use one run of the Gromacs simulation to output the final results. The workflow for this tutorial consists of 2 parts:
- The Gromacs preprocessor (
- The Computational chemistry engine which completes the molecular dynamics simulation (
Simulation software: Gromacs
Now you can monitor the progress of your job from the Status tab. This tab is highlighted in red in the image below. The entire process for submitting this job should take about 22 minutes. Once the job is submitted, it will typically take anywhere from three to seven minutes for the cluster to boot up.
- Because this analysis is entirely run in the cloud, feel free to close your browser window or shut down your computer. You can check on the progress at any time by logging into Rescale and clicking on the Jobs tab. You will receive an email notifying you when the job is completed.
- Rescale’s Live Tailing feature can also be seen below. In this particular example, the files
process_output.logcan be used to monitor the job’s progress.
The Results tab, highlighted in red above, shows all the resulting files that are associated with your job. On this page you can:
- Click on Download to download all the files associated with this job
- View individual files, below a certain size, in your browser by clicking on the View icon in the Actions menu. An example is shown below
Finally, you might like to download the results to compare with the results of your job.