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README.md

EUTOPIA Tutorial: DNA models and OXDNA (Yair Fosado)

Here, you will find information about how to perform Molecular Dynamics simulations of DNA using models with different level of resolution and interactions: Bead-spring, dsDNA and oxDNA. You will learn the advantages of each model and under which situations they can be employed.

Furtheremore, we will discuss how to:

  1. Set initial configurations of DNA molecules with different topology.
  2. Perform Molecular Dynamics simulations with the different models.
  3. Visualise the trajectory from simulations.
  4. Analyse the output from simulations.

Please if you use any of the codes here, do not forget to cite this repository and the corresponding papers in the following links:

bead-spring polymer with Topo2

dsDNA implementation

dsDNA melting

dsDNA supercoling dynamics

oxDNA twist, roll, tilt deformations and dynamics

oxDNA implementation into LAMMPS

DNA nanostar with oxDNA

Requirements

In this section you will find the software neccessary for this tutorial and instructions on how to install it. The tutorial assumes that a LAMMPS executable called lmp_mpi_29Sep2021 exist into this folder (see below for installation).

Also, we recomend to create an alias for ovito. To this end, open a terminal into your home directory and type vim bash.rc. Then add the line:

alias ovito='/home/student/Eutopia-School/Software/ovito-basic-3.7.5-x86_64/bin/./ovito'

Do not forget to replace the path to where you installed ovito.

Git

Git is a distributed version control software. This is, a way to save changes over time without overwriting previous versions. The instructions to install it in Windows, Linux and Mac can be found in the following Link.

Xcode (only for mac users)

You can install Xcode from the App Store.

LAMMPS

In this tutorial we will implement simulations of DNA using oxDNA, a coarse- grained model that is based on force fields tuned to account for several geometrical and thermodynamic features of single and double stranded DNA (in its B form). Details on this model can be found in the extensive literature available online, but for a quick introduction we reccomend this paper.

One important feature of the oxDNA model is that recently it was implemented as a package that can be build into LAMMPS. Here, I mentioned the general steps on how to build LAMMPS with this package (assuming that you are using a computer with either macOS or linux-OS such as Ubuntu). For different operating systems please follow instructions here.

We will work with the current stable release of LAMMPS (29-Sept-2021) that can be installed in the following way: Assuming that you have a terminal located in the home directory, you have to type:

git clone -b stable https://github.com/lammps/lammps.git mylammps

cd mylammps/src/STUBS/

make

cd ../

make yes-molecule yes-asphere yes-CG-DNA yes-extra-molecule yes-rigid yes-misc

make mpi

mv lmp_mpi ~/lmp_mpi_29Sep2021

With this, an executable with the name lmp_mpi_29Sep2021 shoul have been created in your home directory (~/). Copy the executable into this folder, where you downloaded the tutorial.

Ovito

In the tutorial we will learn how to visualize the output generated from simulations. To this end, we will use Ovito a visualization tool that can deal with aspherical particles. This is necessary to capture the planarity of bases in a nucleotide.

To install ovito you just have to follow the instructions in this link. Ovito is very friendly and instructions on installation should be easy to follow. However, here I summarize the steps for installation:

  1. Open this Link

  2. Choose your Operating System

  3. Download the basic version of ovito (free of charge)

  4. Depending on your system:

  • Linux: Extract the downloaded .tar.xz archive file using the tar command: tar xJfv ovito-3.7.0-x86_64.tar.xz. This will create a new sub-directory containing the program files. Change into that directory and start OVITO by running the executable ./bin/ovito.

  • Windows: Run the installer program ovito-x.y.z-win64.exe to install OVITO in a directory of your choice. Note that Windows might ask whether you really want to launch the installer, because it was downloaded from the web and it is not digitally signed.

  • macOS:Double-click the downloaded .dmg disk image file to open it, agree to the program license, and drag the Ovito application bundle into your Applications folder. Then start OVITO by double-clicking the application bundle.

numpy

In ubuntu you can install it by pip3 install numpy

TacoxDNA

More information can be found on this Link

oxView

More information can be found on this Link