# 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](https://developer.nvidia.com/cuda-toolkit) >= 6 * [ARBD](http://bionano.physics.illinois.edu/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](https://dna.physics.ox.ac.uk/index.php/Main_Page) (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](mailto:cmaffeo2@illinois.edu). ```bash # 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 ```