THU2025秋-生物大分子的分子模拟/

Project

Project

1 Basics

1.2 Generating PSF

1.3 Solvating the Protein

1.4 Ubiquitin in a Water Sphere: Simulation with Non-Periodic Boundary Conditions

1.5 Ubiquitin in a Water Box: Simulation with Periodic Boundary Conditions

1.6 Ubiquitin in Generalized Born Implicit Solvent

1.7 Output: Water Sphere Log File

1.8 Analysis of Water Sphere Equilibration

2 Analysis

2.1 Equilibrium

2.1.1 RMSD for individual residues

2.1.2 Maxwell-Boltzmann Energy Distribution

2.1.4 Temperature distribution

2.1.5 Specific Heat - sphere+NVT

2.1.5 Specific Heat - box+NVT

2.2 Non-equilibrium

2.2.1 Heat Diﬀusion