opennucleome

#!/usr/bin/env bash

  

## SBGrid OpenNucleome Example

## https://github.com/ZhangGroup-MITChemistry/OpenNucleome

##

## Run three tutorials from tutorials/init_configs dir 

## Takes ~ 40 minutes on one NVIDIA GeForce GTX 1080 Ti

##

## James Vincent help@sbgrid.org

## Jan 6, 2025

  

export SBGRID_ALLOW=true    # sbgrid internal only

  

echo "SBGrid OpenNucleome Example"

  

## Start SBGrid environment

export SBGRID_ALLOW=true   ## sbgrid dev only

source /programs/sbgrid.shrc

  

## Set OpenNucleome version - from command: $ sbgrid-info -l opennucleome

export OPENNUCLEOME_X=1.3.0

  

## Verify CUDA GPU for OpenNucleome

python.opennucleome -m testInstallation

  

## Get repo

rm -rf ./OpenNucleome

git clone https://github.com/ZhangGroup-MITChemistry/OpenNucleome.git

  

## configs_generation  

cd ./OpenNucleome/tutorials/init_configs/configs_generation/

jupyter.opennucleome nbconvert --to script  ConfigsGeneration.ipynb

python.opennucleome ./ConfigsGeneration.py

  

## configs_relaxation  

cd ../configs_relaxation/

jupyter.opennucleome nbconvert --to script ConfigsRelaxation.ipynb

python.opennucleome ./ConfigsRelaxation.py

  

## configs_selection

cd ../configs_selection

jupyter.opennucleome nbconvert --to script ConfigsSelection.ipynb

python.opennucleome ./ConfigsSelection.py