Introduction¶
GrandFEP : GCMC/FEP - Alchemical free energy calculations in Grand Canonical ensemble
1. Background¶
This Python module is designed to perform free energy calculations with explicit water sampling using OpenMM.
2. Installation¶
2.1. Download the repository¶
git clone https://github.com/huichenggong/GrandFEP.git
cd GrandFEP
2.2. Prepare the environment¶
In the repository root directory, a env.yml file is provided. You can use it to create a conda environment.
Please edit the cuda and MPI version before you run the following command. Use nvidia-smi
to check the hightest cuda version the driver supports. MPI version should follow your cluster
configuration.
# edit cuda and MPI version according to your cluster
mamba env create -f env.yml
mamba activate grandfep_env
pip install .
Or:
mamba create -n grandfep_env python=3.12 numpy scipy pandas openmm openmmtools pymbar-core openmpi=4.1.5 mpi4py parmed cuda-version=12
Check cuda and MPI as what we previously mentioned.
2.3. Later on the cluster¶
source /home/NAME/SOFTWARE/miniforge3/bin/activate grandfep_env
module load openmpi4/gcc/4.1.5
3. Citation¶
The GrandFEP module is released under the MIT licence. The preprint is available on ChemRxiv: Enhancing Relative Binding Free Energy Calculation with Grand Canonical Monte Carlo, Water Swap Monte Carlo, Terminal-Flip Monte Carlo and Replica Exchange Solute Tempering.
