Building a Biphasic System Using GROMACS and VMD Tutorial
The life sciences industry comprises businesses and research that work towards improving the lives of organisms. These companies include biomedical technologies and engineering, the development and manufacturing of pharmaceuticals, and cell biology which may require high performance computing (HPCHPC stands for High-Performance Computing. It refers to the ...). The industry continues to remain at the forefront of addressing the effects of the growing aging population and pandemics such as COVID-19; pharmaceutical companies were able to develop a coronavirus vaccine with the help of HPC.
This tutorial shows you how to build a heterogeneous biphasic system in GROMACS, a molecular dynamics software that simulates proteins, nucleic acids, and lipids, followed by a visualization of the system using Visual Molecular Dynamics (VMD). A heterogeneous biphasic system consists of two different types of molecules in two different types of phases. In this tutorial, the two types of molecules shown are hydrophobic (cyclohexane) and hydrophilic (water). Since cyclohexane is hydrophobic, cyclohexane molecules will repel water molecules. In fact, aqueous biphasic systems can be used in the recovery, extraction, and purification of proteins and antibodies, which can help those in the life sciences industry develop pharmaceuticals and vaccines to help the greater population.
Rescale is able to make the setup of this tutorial significantly easier by simplifying the process to three stages: inputs, software, and hardware. From there, once the job completes, a set of output files are generated in which you can use to visualize the results (either directly, through a post-processing script, or interactively with Rescale Workstations). In doing so, compared to other techniques of manually extracting and purifying proteins, enzymes, and antibodies for biphasic systems or running the simulation on just one software, Rescale allows you to reduce the run time with your choice of hardware, makes the job scalable and efficient, and allows you to create and visualize biphasic systems in one centralized platform.
The expected time to complete the job from start to finish is about fifteen minutes. Alternatively, you can also click the Get Job Results button below, and review the full setup and results for the job immediately. For the purpose of this tutorial, we ran a short and easy job. In the future, one could make a clone of the job and run the job on different hardware and a different number of cores to see how the type of hardware and number of cores affects the time to complete a job. This is easily made doable by performance profiles on Rescale Workstations.
This tutorial is from Dr. Justin A. Lemkul from the Virginia Tech Department of Biochemistry (“GROMACS Tutorial: Building Biphasic Systems”).
Constructing the Biphasic System in GROMACS with Rescale Jobs
In this part of the tutorial, you will be constructing the biphasic system within a box of a given size by filling the box with the cyclohexane and water molecules. Rescale Jobs does the hard computational part of the tutorial and simplifies the setup by prompting you to input the necessary files, software, and hardware.
Configuring Your Job
Go through the following sections to properly configure your job.
Visualization of the Box with Cyclohexane and Water Molecules with Rescale Workstations
Now we will be moving onto visualizing the biphasic system using Visual Molecular Dynamics (VMD) using Rescale Workstations. Rescale Workstations is an interactive environment to post-process a job – it allows you to use the generated output files from a job and visualize the results and allows you to upload coding notebooks and work with them in real time. In this case, we will be doing the former.
Configuring Your Workstation
Go through the following sections to properly configure your workstation.
Monitoring Your Workstation
You can monitor the progress of your workstation from the Workstations home screen.
On the Workstations home screen, you can look at My Workstations to look at all of the workstations you have created as a Rescale user:
Or you can look at Active Workstations to look at the workstations you are currently running:
Further Steps (Optional)
Here are some optional steps that you can do to take the tutorial one step further.
This tutorial shows you how to fill a box of given dimensions with cyclohexane molecules on one half and water molecules on the other half. In the future, you can change certain numbers on each command line to change the dimensions of the box and how much the box is filled with each molecule. In addition, you can control which molecules to put inside the box by changing the input coordinate file and topology file.
Biphasic systems are largely used in the life sciences industry for the development of vaccines and drugs and analysis of biocompatible environments. Completing the tutorial on Rescale helps you leverage high computing power, access to different types of hardware and software to test scalability and diversity for the same simple job, and having the creation and visualization of molecules within the same workspace for easy access for members among a team.