Hossein Ghorbanfekr·Nov 1Building a Linear-Scaling Molecular Dynamics Simulator in Python with C++ Competitive PerformanceThis post will attempt to show how to implement a linear-scaling molecular dynamics (MD) simulator. The main goal is to improve the…
Colby T. Ford, Ph.D.·Oct 26Evaluating AI-Generated Protein Binders with Microsoft’s BioEmu2 ModelEarlier this week, the Microsoft Research AI team released an update to their BioEmu model (called BioEmu2), which enables molecular…
Alexios Gouvielos·Oct 16*511* From Structural Matter to Nuclear Transformation: A Logical Exploration of Hidden Transitions…This text is presented strictly for informational and speculative purposes.
Yobitel·Sep 23How do automated workflows cut simulation setup from days to hours?Automated workflows cut simulation setup from days to hours by removing repeated troubleshooting from the process. With GROMACS, a first…
Dr. Rituparna Hazra·Sep 13From Femtoseconds to Milliseconds: Why Time Matters in Molecular Simulations?Time is precious and crucial. Whether it is about turning up at the examination hall on time, deciding about career choices, or responding…
Aditya Mehta·Aug 14Vacuum Minimization: Cleaning up a starting structure before solvating (MD Simulations)Before a simulation can begin, a researcher has to build a starting structure — often taken from the experimental database — and then…
Hossein Ghorbanfekr·Aug 13How Numba Enables Low-Level CUDA in Python: A Molecular Dynamics ShowcaseIn my previous post, I showed how JAX can be used to implement a GPU-accelerated MD simulator relying on just-in-time compilation…
Chunzhi Wu·Aug 4Relaxing an MD Structure: Three Techniques Before You Hit Runhttps://youtu.be/VRfTi0TCFR8
Chunzhi Wu·Aug 4How to Equilibrate a Polymer System: Two Practical Methodshttps://youtu.be/v6Z4Pz7HJ0U
