Authors:

Selina Lin

Date Created:

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Course Title:

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About Paper:

Researchers use GROMACS and the Vienna Ab initio Simulation Package (VASP) to simulate molecular environments. The simulations are processor-intensive, and high-performance computing (HPC) clusters significantly speed up the process. Although both software packages are available on Anvil via the command line, a graphical user interface (GUI) would benefit users unfamiliar with Linux commands. This project aims to integrate GROMACS and VASP as interactive applications within the Open OnDemand portal on Anvil. The process first involves identifying critical parameters for the molecular simulations. Building an Open OnDemand application requires YAML files for front-end development and job submission to the cluster. Error checking for text inputs and file uploads ensures that users' simulations have a greater chance of running smoothly. Each application utilizes a batch script to run the user's specified simulation. These backend scripts are developed to support different software requirements for CPU and GPU resources. The GROMACS application additionally provides post-analysis data graphs from xvg files, making it easier for researchers to interpret the results. The VASP application can automatically create input files to simplify the job submission process, allowing users to submit their jobs with only the structure file prepared. Creating web-based gateways for the GROMACS and VASP software on Anvil makes it significantly easier for users to run simulations without complex Linux commands. This project sets an example for developing web portals for molecular software packages that other HPC centers can adopt. Keywords: Anvil; Gromacs; Vasp; Open OnDemand; Molecular Dynamics Package

Source:

Purdue University / 2024

Topics:

No topics listed

Co-authors:

Selina Lin