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
  • pandas >= 1.0
  • scadnano >= 0.1 (optional)
  • 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
cmake -S . -B build && (
  cd build
  make -j
)
cd ../../

## Possibly setup python dependencies (you may want to set up a virtual environement) using commands below
# conda install "numpy>=1.14" "scipy>=1.1" "appdirs>=1.4"
# conda install -c conda-forge "mdanalysis>=0.18" "pandas>=1.0"
# pip3 install "cadnano>=2.5.2.1" "scadnano>=0.1" 

git clone https://gitlab.engr.illinois.edu/tbgl/tools/mrdna
cd mrdna
pip3 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