subhajitroy/oxdna repository overview

⁠oxDNA

oxDNA is a simulation code that was initially conceived as an implementation of the coarse-grained DNA model introduced by T. E. Ouldridge, J. P. K. Doye and A. A. Louis. It has been since reworked and it is now an extensible simulation+analysis framework. It natively supports DNA, RNA, Lennard-Jones and patchy particle simulations of different kinds on both single CPU cores and NVIDIA GPUs.

The development of this software has been partially supported by the European Commission through the Marie Skłodowska−Curie Fellowship No.702298-DELTAS, and ONR grant N000142012094.

⁠Docker Images

Here are the most recent updates of the oxDNA docker images with support for both amd64 and arm64 machines. The containers contains both the binaries and as well as the python implementation. Dedicated arm images also has been uploaded to add exclusive support for arm64 devices.

The latest and the cpu build have both amd64 and arm64 support and is compiled on their native device.

⁠Usage

To run the container use

docker run -p 8888:8888 -it --gpus all subhajitroy/oxdna:latest bin/bash

To run a existing folder

docker run -p 8888:8888 -it --rm --gpus all -v "$(pwd):/app" subhajitroy/oxdna:latest oxDNA input

similarly to run oxDNA analysis oat

docker run -p 8888:8888 -it --rm --gpus all -v "$(pwd):/app" subhajitroy/oxdna:latest oat commands

In case one try to run the images using singularity do the following:

• Pull the image singularity pull oxdnaGPU.sif docker://subhajitroy/oxdna:latest
• Run the image with bash singularity run oxdnaGPU.sif /bin/bash
• Prepare the environment source /root/.bashrc
• Navigate to your desire directory and run oxDNA or oat, python module like oat and oxpy should also be working.