Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).
# Create conda environment using environment.yml file
conda env create -f environment.yml
#Clone the github repository
git clone https://github.com/MobleyLab/SeparatedTopologies.gitThe package currently requires an OpenEye license for oechem and oespruce.
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