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tbgl
tools
mrdna
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bd544678
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bd544678
authored
Sep 05, 2019
by
cmaffeo2
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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
```
\ No newline at end of file
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