Commit bd544678 authored by cmaffeo2's avatar cmaffeo2
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Update README.md

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# 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
* [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 $BUILD_DIR
mv ~/Downloads/arbd*.tar.gz .
tar -xzf arbd*.tar.gz
cd arbd/src
make -j
cd ../../
# Setup python dependencies (you may want to set up a virtual environement)
conda install numpy>=1.14 scipy>=1.1 appdirs >= 1.4
conda install -c conda-forge mdanalysis>=0.18
pip install cadnano >= 2.5.2.1
git clone https://gitlab.engr.illinois.edu/tbgl/tools/mrdna
cd mrdna
python setup.py install
cd ..
# Finally update your bashrc so that your shell can find the ARBD binary
echo "PATH=$BUILD_DIR/arbd/src:\$PATH" >> ~/.bashrc
source ~/.bashrc
```
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