Learn how T-REMD enhances conformational sampling in protein–ligand simulations, with setup tips and a GROMACS example workflow.
Aug 3, 2025
Step-by-step workflow for performing PCA and Free Energy Landscape (FEL) analysis from MD simulations with GROMACS.
Jul 9, 2025
A clear workflow for setting up, running, and analyzing a protein–ligand complex simulation using CHARMM36 and TIP3P in GROMACS.
Apr 4, 2025
Overview of key molecular simulation methods — QM, MD, CGMD, MC, BD, LD, DPD — and their strategic applications in drug discovery pipelines.
Jan 8, 2025
Aug 27, 2023
A beginner-friendly guide to how molecular dynamics (MD) simulations work, their applications in structural bioinformatics and materials science, and the insights they provide into complex molecular systems.
Mar 12, 2023
Guidelines for choosing appropriate MD simulation lengths in protein–ligand systems, with key convergence metrics like RMSD, RMSF, and interaction fingerprints.
Jan 9, 2023