Description

Set of scripts for performing several types of MD calculations for polymer physics using openMM software.

Setup

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 [email protected]:4dnucleome/md_soft.git

Install dependencies:

pip install -r requirements.txt

Running simulations

Assuming your config file is named config.ini

run.py -c config.ini

Choosing platform (GPU) to run on

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

Other topics

Preparing initial structure

Your simulation need initial structure. You may find useful scripts for generating initial structures in this repository.

General tips

Distance Constraints on consecutive beads doesnt work with harmonic flat angle. Use harmonic bond instead.

Contact

Michał Kadlof [email protected]