Set of scripts for performing several types of MD calculations for polymer physics using openMM software.
Set virtual env for python 3.7.x using pyenv, with separate virtual env. Compile openMM from sources: How-to
Probably you will need to correct path to python executable, and instalation localization at ccmake.
Clone repo:
git clone git@bitbucket.org:4dnucleome/md_soft.git
Install dependencies:
pip install -r requirements.txt
Assuming your config file is named config.ini
run.py -c config.ini
OpenMM selects the fastest platform to run on automatically. To override the default you can use:
Run on CPU:
run.py -c config.ini --platform CPU
Run on CUDA:
run.py -c config.ini --platform CUDA
Run on CUDA on device 0:
run.py -c config.ini --platform CUDA --device 0
Run on OpenCL:
run.py -c config.ini --platform OpenCL
Your simulation need initial structure. You may find useful scripts for generating initial structures in this repository.
Distance Constraints on consecutive beads doesnt work with harmonic flat angle. Use harmonic bond instead.
Michał Kadlof m.kadlof@cent.uw.edu.pl