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