Molecular dynamics

MD analysis
Molecular dynamics with python

Langevin dynamics

Langevin dynamics
Langevin dynamics with python

Chris Cramer’s lecture

pressure

\(P=\frac{N k T}{V}+\frac{1}{3 V} \sum_{i} \mathbf{r}_{i} \cdot \mathbf{f}_{i}\)

Thermostat

Practical Implementation of Molecular Dynamics Code for Beginners Using Python
Classical Molecular Dynamics code in Python 3.9.0
VX[i] = VX[i] * scale
VY[i] = VY[i] * scale
VZ[i] = VZ[i] * scale

Velocity rescaling

scale = sqrt(T_REF/T_BULK)

Berendsen

scale = sqrt(1+DT*((T_REF/T_BULK)-1)/TAU)

Nose-Hoover thermostat

Understanding Molecular simulaton From Algorithms to Applications (Frenkel & Smit’s): Chapter 6

Appendix E: Algorithm 31 (propagating the chain)
python example: MD Simulation Code of NVT Ensemble using Nose-Hoover Thermostat