Multi-Resolution DNA simulations

A Python3 package that makes it easy to run simulations of DNA nanostructures. The multi-resolution approach provides the benefits of coarse-grained modeling, while resulting in a high-resolution structure suitable for atomistic simulations. Alternatively, the package can be used to initialize simulations using the oxDNA model.

Dependencies

• Linux operating system
• g++ >= 4.8
• CUDA toolkit >= 6
• ARBD simulation engine
• Python >= 3.5 (some users report problems installing mdanalysis; miniconda or conda are recommended)
  • numpy >= 1.14
  • scipy >= 1.1
  • mdanalysis >= 0.18
  • cadnano >= 2.5.2.1
  • appdirs >= 1.4
  • oxDNA (optional)

Installation

First make sure you have the cuda-toolkit installed. First download ARBD through a web browser. The following (untested) script can then be modified and used to install mrdna. Please report issues to Chris Maffeo.

# Customize the following
BUILD_DIR=/path/to/build-dir
export CUDA_PATH=/path/to/cuda-toolkit

# Unpack and build arbd
cd $BUILD_DIR
mv ~/Downloads/arbd*.tar.gz .
tar -xzf arbd*.tar.gz
cd arbd/src
make -j
cd ../../

# Setup python dependencies (you may want to set up a virtual environement)

conda install "numpy>=1.14" "scipy>=1.1" "appdirs>=1.4"
conda install -c conda-forge "mdanalysis>=0.18" 
pip install "cadnano>=2.5.2.1"

git clone https://gitlab.engr.illinois.edu/tbgl/tools/mrdna
cd mrdna
python setup.py install
cd ..

# Finally update your bashrc so that your shell can find the ARBD binary
echo "PATH=$BUILD_DIR/arbd/src:\$PATH" >> ~/.bashrc
source ~/.bashrc