In this tutorial, we will perform energy minimization and equilibration of a simple protein using NAMD [1] & VMD [2]. We are using insulin (PDB ID: 2wfu) for this tutorial.ContentsFiles required1. Downloading PDB file of protein2. Preparing protein file3. Generating a PSF file of protein3.1. Creating protein file without Hydrogens3.2. Generating PSF file3.2.1. Using Automatic … Continue reading Energy minimization and equilibration of simple protein using NAMD & VMD.