byun-jinyoung / openmm_ramd

Allows one to run RAMD simulations in OpenMM

openmm_ramd

Implement random accelerated molecular dynamics (RAMD) in OpenMM.

WARNING: This program is in the early stages and may not perform correctly. Use at your own discretion.

Overview

Random accelerated molecular dynamics (RAMD) was developed to accelerate ligand exit from a binding pocket of a receptor. One can read more about the technique here:

https://kbbox.h-its.org/toolbox/methods/molecular-simulation/random-acceleration-molecular-dynamics-ramd/

This package allows one to run RAMD using OpenMM, optionally generating an output log file that resemble the output produced by the NAMD version of RAMD.

RAMD may be used to generate starting structures along the unbinding pathway, in particular, for the SEEKR2 program. Please see the following links to obtain information about SEEKR2 and how RAMD is used with it:

https://github.com/seekrcentral/seekr2.git https://github.com/seekrcentral/seekrtools.git

In particular, the Seekrtools program HIDR has an option to use RAMD to generate starting structures for SEEKR using the RAMD method.

Quick Install

Dependencies

Many of the dependencies for OpenMM RAMD will be installed alongside SEEKR2, but some must be installed separately, and are installed first, before OpenMM RAMD.

OpenMM

OpenMM is required for the molecular dynamics (MD).

The easiest, quickest way to install the OpenMM is to use Conda. If you don't already have Conda installed, Download Conda with Python version 3.8 from https://conda.io/en/latest/miniconda.html and run the downloaded script and fill out the prompts.

With Conda working, install OpenMM:

conda install -c conda-forge openmm

Install OpenMM RAMD

Once the dependencies are installed, we may install OpenMM RAMD. First, clone this repository and install the package:

git clone https://github.com/seekrcentral/openmm_ramd.git
cd openmm_ramd
python setup.py install

If you get an error stating “No module named ‘Cython’”, this can usually be remedied by installing/updating Cython with:

pip install --upgrade cython

Testing OpenMM RAMD (Optional)

To test OpenMM RAMD, run the following command in the openmm_ramd/ directory:

python setup.py test

Run

OpenMM RAMD is intended to be run as an API, not as a standalone program, therefore a number of example python scripts have been provided in openmm_ramd/openmm_ramd/examples. From within that directory one may try, for example, the following script:

python hsp90_ramd_example.py

One may copy and adapt this script to their own systems and settings.

Copyright

Copyright (c) 2021, Lane Votapka

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.6.