add PyAutoFEP

Dockerfile.gromacs

@@ -125,7 +125,7 @@ nvcc -o test_mpi_cuda test_mpi_cuda.cu -I${CUDA_HOME}/include -I${MPI_HOME}/incl
 EOT
 
 # 安装plumed
-ARG PLUMED_VERSION="2.9.1"
+ARG PLUMED_VERSION="2.9.2"
 ENV PLUMED_VERSION=${PLUMED_VERSION}
 ENV LD_LIBRARY_PATH=/usr/local/plumed/lib:$LD_LIBRARY_PATH
 ENV PATH=/usr/local/plumed:/usr/local/plumed/bin:$PATH
@@ -143,7 +143,7 @@ make install
 EOT
 
 # 安装gromacs
-ARG GROMACS_VERSION="2022.5"
+ARG GROMACS_VERSION="2021.7"
 ENV GROMACS_VERSION=${GROMACS_VERSION}
 ENV GROMACS_HOME=/usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}
 ENV PATH=PATH=$GROMACS_HOME/bin:$PATH
@@ -167,6 +167,23 @@ make install
 echo "source /usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}/bin/GMXRC.bash" >> /root/.bashrc
 EOT
 
+# PyAutoFEP install support version: GROMACS 2021.7
+# GROMACS 2022.5 和 2023 中遇到的“排除原子距离超过截断距离”的问题，确保模拟的稳定性和自由能计算的收敛性。
+# https://github.com/luancarvalhomartins/PyAutoFEP/blob/master/docs/Manual.pdf
+# https://github.com/luancarvalhomartins/PyAutoFEP/tree/master/docs/tutorial01
+ENV CPLUS_INCLUDE_PATH=/usr/include/openbabel3
+ENV LIBRARY_PATH=/usr/lib:/usr/local/lib:${LIBRARY_PATH}
+RUN <<EOT
+#!/bin/bash
+sudo apt-get update
+sudo apt-get install openbabel libopenbabel-dev -y
+sudo apt-get install swig -y
+sudo ln -s /usr/include/openbabel3 /usr/local/include/openbabel3
+/usr/bin/python3 -m pip install ipython rdkit "networkx>2.0,<3.0" alchemlyb==0.6.0 pymbar==3.0.5 openbabel>3.0.0 matplotlib numpy biopython mdanalysis pytest packaging 
+# or openbabel use 2.4.1
+git clone https://github.com/luancarvalhomartins/PyAutoFEP.git 
+EOT
+
 RUN <<EOT
 #!/bin/bash
 apt-get clean && rm -rf /var/lib/apt/lists/*