Molecular Dynamics

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)

Visualization of a similar molecular dynamics simulation using DPPC membranes with an embedded protein. (Image courtesy of Justin Lemkul)

Import Job Setup
Get Job Results

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 (grompp.mdp)
  • The Computational chemistry engine which completes the molecular dynamics simulation (mdrun)

Simulation software: Gromacs

To start using Rescale, go to platform.rescale.com and log in using your account information. Using Rescale requires no download or implementation of additional software. Rescale is browser-based, which allows you to securely access your analyses from your workstation or from your home computer.

From the main screen of the platform, click on the +New Job button at the top left corner of your screen. This will take you to the first of five Setup pages.

First, you need to give the job a name. Because Rescale’s platform saves all your jobs, we recommend you name it something specific so that you can find the job again later. (For example, Tutorial 2: Molecular Dynamics) To change the name of your project, click on the pencil (shown in blue, below) next to the current job name in the top left corner of the window.

Next upload the input file that you want to use by clicking the Choose File button which is highlighted in red below. For this tutorial, you will want to upload the d.dppc.zip file that you downloaded at the start of the tutorial.

On completion, your Input Files setup page should look like that shown below:

Software Settings

Now, you need to select the software module you want to use for your analysis. For this demo, scroll down and click on Gromacs.

When you have selected Gromacs, the Analysis Options will be available.

  • Select version 2016.1 (MPICH, Single Precision, AVX2) from the version selection drop-down menu
  • Next, you need to add the analysis execution command for your project. This is a command that is specific to the software package and input file being used. For this input file and Gromacs, the execution command will be:
cd d.dppc; gmx grompp -v; gmx mdrun

The completed Software Settings should look like those in the image below:

The next step is to select the desired computing hardware for the job. Click on the Hardware Settings icon to do this.

On this page you must select your desired core type and how many cores you need. For this demo, use the drop-down menu to pick the Nickel core type and for Number of Cores, choose one core. Your Hardware Settings screen should look like that shown below:


For this tutorial we omit the optional post processing step. The Review page provides a summary of the job you have set up. It should look like the example shown below. At this stage, you can save and submit the job.

Status

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 d.dppc/md.log and process_output.log can be used to monitor the job’s progress.

Results

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.