Welcome to hairygami_umbrella_sampling’s Documentation

Table of Contents

• Introduction
• oxdna simulation module
  • Simulation
  • SimulationManager
  • GenerateReplicas
  • OxdnaAnalysisTools
  • Analysis
  • Force
  • Observable
• umbrella sampling module
  • BaseUmbrellaSampling
  • ComUmbrellaSampling
  • WhamAnalysis

Introduction

hairygami_umbrella_sampling is a Python interface for running oxDNA umbrella sampling and large throughput simulations. This code is complementary to the article, if you use this code a citation would be appreciated:

• Sample, M., Liu, H., Diep, T., Matthies, M., & Šulc, P. (2023). Hairygami: Analysis of DNA Nanostructures’ Conformational Change Driven by Functionalizable Overhangs. ACS nano.

For more tutorials and examples, please refer to the src folder within this repository.

NVIDIA Multiprocessing Service (MPS)

export CUDA_MPS_PIPE_DIRECTORY=/tmp/mps-pipe
export CUDA_MPS_LOG_DIRECTORY=/tmp/mps-log
mkdir -p $CUDA_MPS_PIPE_DIRECTORY
mkdir -p $CUDA_MPS_LOG_DIRECTORY
nvidia-cuda-mps-control -d

NVIDIA MPS enhances the multiprocessing capabilities of CUDA-enabled GPUs

Prerequisites

• Docker image available on Dockerhub.

docker pull mlsample/hairygamiumbrellasampling:latest
docker run --rm --gpus all -it -p 8888:8888/tcp hairygamiumbrellasampling:latest

or

• Create a virtual python env, Python >= 3.10

• oxDNA installed with Python bindings.

• run ‘pip install .’ within the root directory of this repository.

Indices and Tables

• Index

• Module Index

• Search Page