Introduction¶
GrandFEP : GCMC/FEP - Alchemical free energy calculations in Grand Canonical ensemble
1. Background¶
This Python module is designed to perform grand canonical Monte Carlo (GCMC) and free energy calculations 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.
mamba env create -f env.yml
# edit cuda and MPI version according to your cluster
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 cudatoolkit=11.8
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. I hope my publication will come soon.
