About GROMACS-LS

What is GROMACS-LS?

GROMACS-LS is a research fork of the widely used molecular dynamics simulation GROMACS that aims to implement local stress and elasticity calculations via the MDStress Library.

Why GROMACS-LS?

GROMACS-LS offers simple stress and elasticity calculations that can be computed during a simulation, a feature which is missing from the base GROMACS software. Other highlights of GROMACS-LS:

• Uses the autodiff library to easily compute up to 4-body potentials
• Calculations for 1-, 2-, and 3-dimensional systems
• SIMD parallelized stress and elasticity calculations, minimizing additional simulation time
• Recently updated to be based on the 2025.4 branch of GROMACS (up from 2016.3)

Demo video

How to use GROMACS-LS

Steps to install and use GROMACS-LS can be found on the GitHub page, GROMACS-LS. The primary dependency for GROMACS-LS is the MDStress library. Other dependencies include:

• FFTW3 (double precision, libfftw3.so)
• CMake
• Python 3 with Numpy and Scipy (to use the tensortools analysis tool)

Team Members

Capstone group

Abdul Raziq

Abdul Raziq is a junior at Oregon State University studying Computer Science with a focus on performance engineering and scientific computing. His work centers on optimizing high-performance systems, including molecular dynamics simulations. As part of the GROMACS-LS capstone project, he contributes to performance optimization, SIMD acceleration, and integration with advanced libraries such as MDStress and etc

Portfolio: https://web.engr.oregonstate.edu/~razika/Personal%20Portfolio/ GitHub: https://github.com/ARB726

Nathaniel Chappelle

Nathaniel is a senior at Oregon State University with industry experience in the semiconductor field, spanning both industrial automation and electronic design automation (EDA). As part of the GROMACS-LS project, he primarily contributed to porting the codebase from version 2016.3 to 2025.4, working across both the simulation harness and the compute kernels.

Links:

• chappelle.dev
• codeberg.org

Joo Wang Lee

Joo Wang Lee is a senior at Oregon State University majoring in Applied Computer Science with a focus in Data Science.

Finlay Curtiss

Finlay is a senior at Oregon State University studying Computer Science and Environmental Science.

Project partner

Dr. Juan Vanegas

Associate Professor of Biochemistry & Biophysics at Oregon State University