Fundamentals of Classical Molecular Dynamics

Leandro Martínez
Instituto de Quimica, Universidade Estadual de Campinas (UNICAMP)
http://m3g.iqm.unicamp.br

This tutorial contains explanations for running and analyzing Molecular Dynamics and Monte Carlo simulations of a simple two-dimensional system. The goal is for the student to become familiar with various technical details involved in performing simulations and their limitations.

1.1. Installing FundamentosDMC.jl

Install the Julia interpreter using the juliaup tool. Julia version 1.9 will be installed.

Tip

By pressing ] at the Julia prompt, you will access the package manager (a blue prompt). A sequence like julia> ] add Package is not meant to be copied and pasted as-is.
All other commands in this tutorial can be copied and pasted directly, including the julia> prompt, which is removed automatically.

Run the interpreter. We will create an environment where we will install the necessary packages:

julia> ] activate @FundamentosDMC

(the ] will take you to the package management prompt, "(@v1.9) pkg>", where activate ... should be run) Press backspace to return to the julia> prompt.

Then, install the packages:

julia> ] add https://github.com/m3g/FundamentosDMC.jl, Plots, LsqFit

This process may take a couple of minutes and will compile and install all packages in the @FundamentosDMC environment.

1.2. Installing VMD

We will use VMD for trajectory visualization. Make sure to have it installed as well.

1.3. Code

Julia is a high-performance, dynamic programming language with a fairly simple syntax (read here). All the code for this course is available in the repository https://github.com/m3g/FundamentosDMC.jl, and reading through it will be encouraged as we progress through the tutorial.

The code here is reasonably efficient for carrying out the tutorial, but is not optimized for maximum performance, so that it is easier to read.

1.4. Complete summary code

Packages can be installed from a script with:

import Pkg
Pkg.activate("FundamentosDMC", shared=true)
Pkg.add(url="https://github.com/m3g/FundamentosDMC.jl")
Pkg.add("Plots")
Pkg.add("LsqFit")

1.5. Graphical interface

In addition to running simulations from the Julia REPL as described in this tutorial, FundamentosDMC.jl provides an interactive graphical interface, built on GLMakie. It can be used to follow, live, the execution of simulations in the different ensembles covered here — the microcanonical (NVE) simulation and the NVT simulations with the isokinetic, Berendsen, and Langevin thermostats — as well as to follow Monte Carlo simulations, showing the motion of the particles together with the potential, kinetic and total energies, and the temperature. All the simulation and system parameters can be set directly in the interface.

To use it, install and load GLMakie in addition to FundamentosDMC:

julia> import Pkg; Pkg.add("GLMakie")

julia> using FundamentosDMC

julia> import GLMakie

julia> simulate_gui()