diff --git a/Dockerfile.gromacs b/Dockerfile.gromacs index b1f534e..39ea516 100755 --- a/Dockerfile.gromacs +++ b/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 <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 <