SeparatedTopologies

Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).

Installation

# Create conda environment using environment.yml file
conda env create -f environment.yml

#Clone the github repository
git clone https://github.com/MobleyLab/SeparatedTopologies.git

The package currently requires an OpenEye license for oechem and oespruce.

Usage

Example python script for setting up topology and coordinate files

• for SepTop in the complex phase: prep_SepTop_complex.py
• for SepTop in the solvent phase: prep_SepTop_solvent.py
• for absolute hydration free energy calculations: prep_solvent_absolute.py

Example MDP files can be found in the folder MDP_files