diff --git a/Dockerfile.gromacs b/Dockerfile.gromacs
index 39ea516..0eaf629 100755
--- a/Dockerfile.gromacs
+++ b/Dockerfile.gromacs
@@ -1,194 +1,194 @@
-# syntax=docker/dockerfile:1
-# NOTE: Building this image require's docker version >= 23.0.
-#
-# For reference:
-# - https://docs.docker.com/build/dockerfile/frontend/#stable-channel
-ARG TAG_VERSION="12.4.1"
-FROM nvidia/cuda:${TAG_VERSION}-cudnn-devel-ubuntu22.04
-ARG HTTP_PROXY
-ARG HTTPS_PROXY
-ENV http_proxy=${HTTP_PROXY}
-ENV https_proxy=${HTTPS_PROXY}
-ARG DEBIAN_FRONTEND="noninteractive"
-ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
-ARG ROOT_PASSWD="root"
-ENV ROOT_PASSWD=${ROOT_PASSWD}
-ENV SSH_PORT=2222
-WORKDIR /root
-SHELL ["/bin/bash", "-c"]
-
-# base tools
-RUN <<EOT
-#!/bin/bash
-apt-get update
-apt-get install -y libgl1-mesa-glx bash-completion wget curl htop jq vim bash libaio-dev build-essential openssh-server openssh-client python3 python3-pip python3-venv bzip2 screen
-apt-get install -y --no-install-recommends software-properties-common build-essential autotools-dev nfs-common pdsh cmake g++ gcc curl wget vim tmux emacs less unzip htop iftop iotop ca-certificates openssh-client openssh-server rsync iputils-ping net-tools sudo llvm-dev re2c
-add-apt-repository ppa:git-core/ppa -y
-apt-get install -y git libnuma-dev wget
-pip install pipx
-pipx install nvitop
-pipx ensurepath 
-. ~/.bashrc
-# Configure SSH for password and public key authentication
-mkdir ~/.ssh
-# 创建或覆盖 SSH 配置文件 ~/.ssh/config
-# - Host *: 针对所有主机的通用配置
-# - ForwardAgent yes: 启用 SSH 代理转发，允许通过本地的 SSH 代理进行身份验证
-# - StrictHostKeyChecking no: 禁用主机密钥检查，自动接受新的主机密钥（适用于自动化环境）
-printf "Host * \n    ForwardAgent yes\nHost *\n    StrictHostKeyChecking no" > ~/.ssh/config
-cp /etc/ssh/sshd_config /etc/ssh/sshd_config.bak
-sed -i 's/#PermitRootLogin prohibit-password/PermitRootLogin yes/' /etc/ssh/sshd_config
-sed -i 's/#PasswordAuthentication yes/PasswordAuthentication yes/' /etc/ssh/sshd_config
-sed -i 's/#PubkeyAuthentication yes/PubkeyAuthentication yes/' /etc/ssh/sshd_config
-sed -i 's/^\(\s*\)GSSAPIAuthentication yes/\1GSSAPIAuthentication no/' /etc/ssh/ssh_config
-sed -i "s/^#Port 22/Port ${SSH_PORT}/" /etc/ssh/sshd_config
-sudo sed -i "s/#   Port 22/Port ${SSH_PORT}/" /etc/ssh/ssh_config
-ssh-keygen -t rsa -b 4096 -f /root/.ssh/id_rsa -N "" <<< y
-cat ~/.ssh/id_rsa.pub >> ~/.ssh/auth
-cat /root/.ssh/id_rsa.pub >> /root/.ssh/authorized_keys
-cat /root/.ssh/id_rsa.pub >> /root/.ssh/authorized_keys2
-chmod 600 /root/.ssh/authorized_keys
-chmod 600 /root/.ssh/authorized_keys2
-mkdir /var/run/sshd
-echo "root:${ROOT_PASSWD}" | chpasswd
-mkdir -p ~/.pip
-# install pixi
-curl -fsSL https://pixi.sh/install.sh | bash
-EOT
-
-ARG FFTW_VERSION="3.3.10"
-ENV FFTW_VERSION=${FFTW_VERSION}
-ENV PATH=/usr/local/fftw:$PATH
-# 安装fftw
-RUN <<EOT
-#!/bin/bash
-wget http://www.fftw.org/fftw-${FFTW_VERSION}.tar.gz
-tar zxvf fftw-${FFTW_VERSION}.tar.gz
-cd fftw-${FFTW_VERSION}
-./configure --prefix=/usr/local/fftw --enable-sse2 --enable-avx --enable-float --enable-avx2 --enable-shared  # 若CPU支持AVX512指令集，且有多于1个AVX512 FMA单元，则可加上--enable-avx512以进一步提升性能
-make -j$(nproc)
-make install
-EOT
-
-# 安装openmpi
-ENV MPI_HOME=/usr/local/openmpi
-ENV PATH=${MPI_HOME}/bin:/usr/bin:$PATH
-ENV LD_LIBRARY_PATH=/usr/local/cuda/lib64:${MPI_HOME}/lib:/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH
-ENV LIBRARY_PATH=/usr/local/cuda/lib64:${LIBRARY_PATH}
-ENV CPATH=/usr/local/cuda/include:${MPI_HOME}/include:${CUDA_HOME}/include:$CPATH
-# export C_INCLUDE_PATH=/usr/local/cuda/include:$C_INCLUDE_PATH
-# export LIBRARY_PATH=/usr/local/cuda/lib64:$LIBRARY_PATH
-# export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
-RUN <<EOT
-#!/bin/bash
-apt update &&  apt install -y autoconf automake libtool flex
-/usr/bin/python3 -m pip install cython
-git clone --recursive https://github.com/open-mpi/ompi.git
-cd ompi
-git checkout main
-# make clean
-# make distclean
-./autogen.pl
-mkdir build
-cd build
-../configure --with-cuda=/usr/local/cuda --enable-python-bindings --enable-mpirun-prefix-by-default --prefix=${MPI_HOME} --with-python=/usr/bin/python3
-make -j$(nproc)
-make install
-# 验证CUDA支持
-cat <<EOF > ./test_mpi_cuda.cu
-#include <mpi.h>
-#include <cuda_runtime.h>
-#include <stdio.h>
-
-__global__ void hello_cuda() {
-    printf("Hello from CUDA kernel! Thread id: %d\n", threadIdx.x);
-}
-
-int main(int argc, char **argv) {
-    MPI_Init(&argc, &argv);
-
-    int rank;
-    MPI_Comm_rank(MPI_COMM_WORLD, &rank);
-
-    printf("Hello from MPI process %d!\n", rank);
-
-    // Launch CUDA kernel
-    hello_cuda<<<1, 10>>>();
-    cudaDeviceSynchronize();  // Wait for the CUDA kernel to finish
-
-    MPI_Finalize();
-    return 0;
-}
-EOF
-nvcc -o test_mpi_cuda test_mpi_cuda.cu -I${CUDA_HOME}/include -I${MPI_HOME}/include -L${MPI_HOME}/lib -lcudart -lmpi
-# mpirun --allow-run-as-root -np 2 ./test_mpi_cuda
-EOT
-
-# 安装plumed
-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:$PATH
-RUN <<EOT
-#!/bin/bash
-# git clone https://github.com/plumed/plumed2
-# cd plumed2
-# git checkout v${PLUMED_VERSION}
-curl -L -o plumed-${PLUMED_VERSION}.tar.gz https://github.com/plumed/plumed2/releases/download/v${PLUMED_VERSION}/plumed-${PLUMED_VERSION}.tgz
-tar zxvf plumed-${PLUMED_VERSION}.tar.gz
-cd plumed-${PLUMED_VERSION}
-./configure --prefix=/usr/local/plumed
-make -j$(nproc)
-make install 
-EOT
-
-# 安装gromacs
-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:$PATH
-RUN <<EOT
-#!/bin/bash
-wget -c https://ftp.gromacs.org/gromacs/gromacs-${GROMACS_VERSION}.tar.gz
-tar zxvf gromacs-${GROMACS_VERSION}.tar.gz
-cd gromacs-${GROMACS_VERSION}
-### patch the plumed
-# plumed-patch -p
-plumed-patch -p -e gromacs-${GROMACS_VERSION}
-mkdir build
-cd build
-cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION} \
-         -DGMX_BUILD_OWN_FFTW=ON \
-         -DREGRESSIONTEST_DOWNLOAD=ON \
-         -DGMX_GPU=CUDA \
-         -DGMX_MPI=ON
-make -j$(nproc)
-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:${LIBRARY_PATH}
-RUN <<EOT
-#!/bin/bash
-sudo apt-get update
-sudo apt-get install openbabel libopenbabel-dev -y
-sudo apt-get install swig -y
-sudo ln -s /usr/include/openbabel3 /usr/local/include/openbabel3
-/usr/bin/python3 -m pip install ipython rdkit "networkx>2.0,<3.0" alchemlyb==0.6.0 pymbar==3.0.5 openbabel>3.0.0 matplotlib numpy biopython mdanalysis pytest packaging 
-# or openbabel use 2.4.1
-git clone https://github.com/luancarvalhomartins/PyAutoFEP.git 
-EOT
-
-RUN <<EOT
-#!/bin/bash
-apt-get clean && rm -rf /var/lib/apt/lists/*
-EOT
-
-EXPOSE 2222
-
-CMD ["/usr/sbin/sshd", "-D"]
+# syntax=docker/dockerfile:1.3-labs
+# NOTE: Building this image require's docker version >= 23.0.
+#
+# For reference:
+# - https://docs.docker.com/build/dockerfile/frontend/#stable-channel
+ARG TAG_VERSION="12.4.1"
+FROM nvidia/cuda:${TAG_VERSION}-cudnn-devel-ubuntu22.04
+ARG HTTP_PROXY
+ARG HTTPS_PROXY
+ENV http_proxy=${HTTP_PROXY}
+ENV https_proxy=${HTTPS_PROXY}
+ARG DEBIAN_FRONTEND="noninteractive"
+ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
+ARG ROOT_PASSWD="root"
+ENV ROOT_PASSWD=${ROOT_PASSWD}
+ENV SSH_PORT=2222
+WORKDIR /root
+SHELL ["/bin/bash", "-c"]
+
+# base tools
+RUN <<EOT
+#!/bin/bash
+apt-get update
+apt-get install -y libgl1-mesa-glx bash-completion wget curl htop jq vim bash libaio-dev build-essential openssh-server openssh-client python3 python3-pip python3-venv bzip2 screen
+apt-get install -y --no-install-recommends software-properties-common build-essential autotools-dev nfs-common pdsh cmake g++ gcc curl wget vim tmux emacs less unzip htop iftop iotop ca-certificates openssh-client openssh-server rsync iputils-ping net-tools sudo llvm-dev re2c
+add-apt-repository ppa:git-core/ppa -y
+apt-get install -y git libnuma-dev wget
+pip install pipx
+pipx install nvitop
+pipx ensurepath 
+. ~/.bashrc
+# Configure SSH for password and public key authentication
+mkdir ~/.ssh
+# 创建或覆盖 SSH 配置文件 ~/.ssh/config
+# - Host *: 针对所有主机的通用配置
+# - ForwardAgent yes: 启用 SSH 代理转发，允许通过本地的 SSH 代理进行身份验证
+# - StrictHostKeyChecking no: 禁用主机密钥检查，自动接受新的主机密钥（适用于自动化环境）
+printf "Host * \n    ForwardAgent yes\nHost *\n    StrictHostKeyChecking no" > ~/.ssh/config
+cp /etc/ssh/sshd_config /etc/ssh/sshd_config.bak
+sed -i 's/#PermitRootLogin prohibit-password/PermitRootLogin yes/' /etc/ssh/sshd_config
+sed -i 's/#PasswordAuthentication yes/PasswordAuthentication yes/' /etc/ssh/sshd_config
+sed -i 's/#PubkeyAuthentication yes/PubkeyAuthentication yes/' /etc/ssh/sshd_config
+sed -i 's/^\(\s*\)GSSAPIAuthentication yes/\1GSSAPIAuthentication no/' /etc/ssh/ssh_config
+sed -i "s/^#Port 22/Port ${SSH_PORT}/" /etc/ssh/sshd_config
+sudo sed -i "s/#   Port 22/Port ${SSH_PORT}/" /etc/ssh/ssh_config
+ssh-keygen -t rsa -b 4096 -f /root/.ssh/id_rsa -N "" <<< y
+cat ~/.ssh/id_rsa.pub >> ~/.ssh/auth
+cat /root/.ssh/id_rsa.pub >> /root/.ssh/authorized_keys
+cat /root/.ssh/id_rsa.pub >> /root/.ssh/authorized_keys2
+chmod 600 /root/.ssh/authorized_keys
+chmod 600 /root/.ssh/authorized_keys2
+mkdir /var/run/sshd
+echo "root:${ROOT_PASSWD}" | chpasswd
+mkdir -p ~/.pip
+# install pixi
+curl -fsSL https://pixi.sh/install.sh | bash
+EOT
+
+ARG FFTW_VERSION="3.3.10"
+ENV FFTW_VERSION=${FFTW_VERSION}
+ENV PATH=/usr/local/fftw:$PATH
+# 安装fftw
+RUN <<EOT
+#!/bin/bash
+wget http://www.fftw.org/fftw-${FFTW_VERSION}.tar.gz
+tar zxvf fftw-${FFTW_VERSION}.tar.gz
+cd fftw-${FFTW_VERSION}
+./configure --prefix=/usr/local/fftw --enable-sse2 --enable-avx --enable-float --enable-avx2 --enable-shared  # 若CPU支持AVX512指令集，且有多于1个AVX512 FMA单元，则可加上--enable-avx512以进一步提升性能
+make -j$(nproc)
+make install
+EOT
+
+# 安装openmpi
+ENV MPI_HOME=/usr/local/openmpi
+ENV PATH=${MPI_HOME}/bin:/usr/bin:$PATH
+ENV LD_LIBRARY_PATH=/usr/local/cuda/lib64:${MPI_HOME}/lib:/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH
+ENV LIBRARY_PATH=/usr/local/cuda/lib64:${LIBRARY_PATH}
+ENV CPATH=/usr/local/cuda/include:${MPI_HOME}/include:${CUDA_HOME}/include:$CPATH
+# export C_INCLUDE_PATH=/usr/local/cuda/include:$C_INCLUDE_PATH
+# export LIBRARY_PATH=/usr/local/cuda/lib64:$LIBRARY_PATH
+# export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
+RUN <<EOT
+#!/bin/bash
+apt update &&  apt install -y autoconf automake libtool flex
+/usr/bin/python3 -m pip install cython
+git clone --recursive https://github.com/open-mpi/ompi.git
+cd ompi
+git checkout main
+# make clean
+# make distclean
+./autogen.pl
+mkdir build
+cd build
+../configure --with-cuda=/usr/local/cuda --enable-python-bindings --enable-mpirun-prefix-by-default --prefix=${MPI_HOME} --with-python=/usr/bin/python3
+make -j$(nproc)
+make install
+# 验证CUDA支持
+cat <<EOF > ./test_mpi_cuda.cu
+#include <mpi.h>
+#include <cuda_runtime.h>
+#include <stdio.h>
+
+__global__ void hello_cuda() {
+    printf("Hello from CUDA kernel! Thread id: %d\n", threadIdx.x);
+}
+
+int main(int argc, char **argv) {
+    MPI_Init(&argc, &argv);
+
+    int rank;
+    MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+
+    printf("Hello from MPI process %d!\n", rank);
+
+    // Launch CUDA kernel
+    hello_cuda<<<1, 10>>>();
+    cudaDeviceSynchronize();  // Wait for the CUDA kernel to finish
+
+    MPI_Finalize();
+    return 0;
+}
+EOF
+nvcc -o test_mpi_cuda test_mpi_cuda.cu -I${CUDA_HOME}/include -I${MPI_HOME}/include -L${MPI_HOME}/lib -lcudart -lmpi
+# mpirun --allow-run-as-root -np 2 ./test_mpi_cuda
+EOT
+
+# 安装plumed
+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:$PATH
+RUN <<EOT
+#!/bin/bash
+# git clone https://github.com/plumed/plumed2
+# cd plumed2
+# git checkout v${PLUMED_VERSION}
+curl -L -o plumed-${PLUMED_VERSION}.tar.gz https://github.com/plumed/plumed2/releases/download/v${PLUMED_VERSION}/plumed-${PLUMED_VERSION}.tgz
+tar zxvf plumed-${PLUMED_VERSION}.tar.gz
+cd plumed-${PLUMED_VERSION}
+./configure --prefix=/usr/local/plumed
+make -j$(nproc)
+make install 
+EOT
+
+# 安装gromacs
+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:$PATH
+RUN <<EOT
+#!/bin/bash
+wget -c https://ftp.gromacs.org/gromacs/gromacs-${GROMACS_VERSION}.tar.gz
+tar zxvf gromacs-${GROMACS_VERSION}.tar.gz
+cd gromacs-${GROMACS_VERSION}
+### patch the plumed
+# plumed-patch -p
+plumed-patch -p -e gromacs-${GROMACS_VERSION}
+mkdir build
+cd build
+cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION} \
+         -DGMX_BUILD_OWN_FFTW=ON \
+         -DREGRESSIONTEST_DOWNLOAD=ON \
+         -DGMX_GPU=CUDA \
+         -DGMX_MPI=ON
+make -j$(nproc)
+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:${LIBRARY_PATH}
+RUN <<EOT
+#!/bin/bash
+sudo apt-get update
+sudo apt-get install openbabel libopenbabel-dev -y
+sudo apt-get install swig -y
+sudo ln -s /usr/include/openbabel3 /usr/local/include/openbabel3
+/usr/bin/python3 -m pip install ipython rdkit "networkx>2.0,<3.0" alchemlyb==0.6.0 pymbar==3.0.5 openbabel>3.0.0 matplotlib numpy biopython mdanalysis pytest packaging 
+# or openbabel use 2.4.1
+git clone https://github.com/luancarvalhomartins/PyAutoFEP.git 
+EOT
+
+RUN <<EOT
+#!/bin/bash
+apt-get clean && rm -rf /var/lib/apt/lists/*
+EOT
+
+EXPOSE 2222
+
+CMD ["/usr/sbin/sshd", "-D"]
diff --git a/Dockerfile.gromacs_amber b/Dockerfile.gromacs_amber
index 4182c2e..d4971f2 100755
--- a/Dockerfile.gromacs_amber
+++ b/Dockerfile.gromacs_amber
@@ -1,192 +1,192 @@
-# syntax=docker/dockerfile:1
-# NOTE: Building this image require's docker version >= 23.0.
-#
-# For reference:
-# - https://docs.docker.com/build/dockerfile/frontend/#stable-channel
-ARG TAG_VERSION="12.4.1"
-FROM nvidia/cuda:${TAG_VERSION}-cudnn-devel-ubuntu22.04
-ARG HTTP_PROXY
-ARG HTTPS_PROXY
-ENV http_proxy=${HTTP_PROXY}
-ENV https_proxy=${HTTPS_PROXY}
-ARG DEBIAN_FRONTEND="noninteractive"
-ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
-ARG ROOT_PASSWD="root"
-ENV ROOT_PASSWD=${ROOT_PASSWD}
-ENV SSH_PORT=2222
-WORKDIR /root
-SHELL ["/bin/bash", "-c"]
-
-# base tools
-RUN <<EOT
-#!/bin/bash
-apt-get update
-apt-get install -y libgl1-mesa-glx bash-completion wget curl htop jq vim bash libaio-dev build-essential openssh-server openssh-client python3 python3-pip python3-venv bzip2 screen
-apt-get install -y --no-install-recommends software-properties-common build-essential autotools-dev nfs-common pdsh cmake g++ gcc curl wget vim tmux emacs less unzip htop iftop iotop ca-certificates openssh-client openssh-server rsync iputils-ping net-tools sudo llvm-dev re2c
-add-apt-repository ppa:git-core/ppa -y
-apt-get install -y git libnuma-dev wget
-pip install pipx
-pipx install nvitop
-pipx ensurepath 
-. ~/.bashrc
-# Configure SSH for password and public key authentication
-mkdir ~/.ssh
-# 创建或覆盖 SSH 配置文件 ~/.ssh/config
-# - Host *: 针对所有主机的通用配置
-# - ForwardAgent yes: 启用 SSH 代理转发，允许通过本地的 SSH 代理进行身份验证
-# - StrictHostKeyChecking no: 禁用主机密钥检查，自动接受新的主机密钥（适用于自动化环境）
-printf "Host * \n    ForwardAgent yes\nHost *\n    StrictHostKeyChecking no" > ~/.ssh/config
-cp /etc/ssh/sshd_config /etc/ssh/sshd_config.bak
-sed -i 's/#PermitRootLogin prohibit-password/PermitRootLogin yes/' /etc/ssh/sshd_config
-sed -i 's/#PasswordAuthentication yes/PasswordAuthentication yes/' /etc/ssh/sshd_config
-sed -i 's/#PubkeyAuthentication yes/PubkeyAuthentication yes/' /etc/ssh/sshd_config
-sed -i 's/^\(\s*\)GSSAPIAuthentication yes/\1GSSAPIAuthentication no/' /etc/ssh/ssh_config
-sed -i "s/^#Port 22/Port ${SSH_PORT}/" /etc/ssh/sshd_config
-sudo sed -i "s/#   Port 22/Port ${SSH_PORT}/" /etc/ssh/ssh_config
-ssh-keygen -t rsa -b 4096 -f /root/.ssh/id_rsa -N "" <<< y
-cat ~/.ssh/id_rsa.pub >> ~/.ssh/auth
-cat /root/.ssh/id_rsa.pub >> /root/.ssh/authorized_keys
-cat /root/.ssh/id_rsa.pub >> /root/.ssh/authorized_keys2
-chmod 600 /root/.ssh/authorized_keys
-chmod 600 /root/.ssh/authorized_keys2
-mkdir /var/run/sshd
-echo "root:${ROOT_PASSWD}" | chpasswd
-mkdir -p ~/.pip
-# install pixi
-curl -fsSL https://pixi.sh/install.sh | bash
-EOT
-
-ARG FFTW_VERSION="3.3.10"
-ENV FFTW_VERSION=${FFTW_VERSION}
-ENV PATH=/usr/local/fftw:$PATH
-# 安装fftw
-RUN <<EOT
-#!/bin/bash
-wget http://www.fftw.org/fftw-${FFTW_VERSION}.tar.gz
-tar zxvf fftw-${FFTW_VERSION}.tar.gz
-cd fftw-${FFTW_VERSION}
-./configure --prefix=/usr/local/fftw --enable-sse2 --enable-avx --enable-float --enable-avx2 --enable-shared  # 若CPU支持AVX512指令集，且有多于1个AVX512 FMA单元，则可加上--enable-avx512以进一步提升性能
-make -j$(nproc)
-make install
-EOT
-
-# 安装openmpi
-ENV MPI_HOME=/usr/local/openmpi
-ENV PATH=${MPI_HOME}/bin:/usr/bin:$PATH
-ENV LD_LIBRARY_PATH=/usr/local/cuda/lib64:${MPI_HOME}/lib:/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH
-ENV LIBRARY_PATH=/usr/local/cuda/lib64:${LIBRARY_PATH}
-ENV CPATH=/usr/local/cuda/include:${MPI_HOME}/include:${CUDA_HOME}/include:$CPATH
-# export C_INCLUDE_PATH=/usr/local/cuda/include:$C_INCLUDE_PATH
-# export LIBRARY_PATH=/usr/local/cuda/lib64:$LIBRARY_PATH
-# export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
-RUN <<EOT
-#!/bin/bash
-apt update &&  apt install -y autoconf automake libtool flex
-/usr/bin/python3 -m pip install cython
-git clone --recursive https://github.com/open-mpi/ompi.git
-cd ompi
-git checkout main
-# make clean
-# make distclean
-./autogen.pl
-mkdir build
-cd build
-../configure --with-cuda=/usr/local/cuda --enable-python-bindings --enable-mpirun-prefix-by-default --prefix=${MPI_HOME} --with-python=/usr/bin/python3
-make -j$(nproc)
-make install
-# 验证CUDA支持
-cat <<EOF > ./test_mpi_cuda.cu
-#include <mpi.h>
-#include <cuda_runtime.h>
-#include <stdio.h>
-
-__global__ void hello_cuda() {
-    printf("Hello from CUDA kernel! Thread id: %d\n", threadIdx.x);
-}
-
-int main(int argc, char **argv) {
-    MPI_Init(&argc, &argv);
-
-    int rank;
-    MPI_Comm_rank(MPI_COMM_WORLD, &rank);
-
-    printf("Hello from MPI process %d!\n", rank);
-
-    // Launch CUDA kernel
-    hello_cuda<<<1, 10>>>();
-    cudaDeviceSynchronize();  // Wait for the CUDA kernel to finish
-
-    MPI_Finalize();
-    return 0;
-}
-EOF
-nvcc -o test_mpi_cuda test_mpi_cuda.cu -I${CUDA_HOME}/include -I${MPI_HOME}/include -L${MPI_HOME}/lib -lcudart -lmpi
-# mpirun --allow-run-as-root -np 2 ./test_mpi_cuda
-EOT
-
-# 安装plumed
-ARG PLUMED_VERSION="2.9.1"
-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:$PATH
-RUN <<EOT
-#!/bin/bash
-# git clone https://github.com/plumed/plumed2
-# cd plumed2
-# git checkout v${PLUMED_VERSION}
-curl -L -o plumed-${PLUMED_VERSION}.tar.gz https://github.com/plumed/plumed2/releases/download/v${PLUMED_VERSION}/plumed-${PLUMED_VERSION}.tgz
-tar zxvf plumed-${PLUMED_VERSION}.tar.gz
-cd plumed-${PLUMED_VERSION}
-./configure --prefix=/usr/local/plumed
-make -j$(nproc)
-make install 
-EOT
-
-# 安装gromacs
-ARG GROMACS_VERSION="2022.5"
-ENV GROMACS_VERSION=${GROMACS_VERSION}
-ENV GROMACS_HOME=/usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}
-ENV PATH=PATH=$GROMACS_HOME/bin:$PATH
-RUN <<EOT
-#!/bin/bash
-wget -c https://ftp.gromacs.org/gromacs/gromacs-${GROMACS_VERSION}.tar.gz
-tar zxvf gromacs-${GROMACS_VERSION}.tar.gz
-cd gromacs-${GROMACS_VERSION}
-### patch the plumed
-# plumed-patch -p
-plumed-patch -p -e gromacs-${GROMACS_VERSION}
-mkdir build
-cd build
-cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION} \
-         -DGMX_BUILD_OWN_FFTW=ON \
-         -DREGRESSIONTEST_DOWNLOAD=ON \
-         -DGMX_GPU=CUDA \
-         -DGMX_MPI=ON
-make -j$(nproc)
-make install 
-echo "source /usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}/bin/GMXRC.bash" >> /root/.bashrc
-EOT
-
-COPY file/Amber24.tar.bz2 file/AmberTools24.tar.bz2 /root
-
-ENV DOWNLOAD_MINICONDA="False"
-# install ambertools
-RUN <<EOT
-#!/bin/bash
-python3 -m pip install numpy scipy matplotlib
-# 解压 Amber24
-tar -xjf Amber24.tar.bz2
-# 解压 AmberTools24
-tar -xjf AmberTools24.tar.bz2
-# 清理解压后的 .tar.bz2 文件（可选）
-rm Amber24.tar.bz2 AmberTools24.tar.bz2
-EOT
-
-RUN <<EOT
-#!/bin/bash
-apt-get clean && rm -rf /var/lib/apt/lists/*
-EOT
-
-EXPOSE 2222
-
-CMD ["/usr/sbin/sshd", "-D"]
+# syntax=docker/dockerfile:1
+# NOTE: Building this image require's docker version >= 23.0.
+#
+# For reference:
+# - https://docs.docker.com/build/dockerfile/frontend/#stable-channel
+ARG TAG_VERSION="12.4.1"
+FROM nvidia/cuda:${TAG_VERSION}-cudnn-devel-ubuntu22.04
+ARG HTTP_PROXY
+ARG HTTPS_PROXY
+ENV http_proxy=${HTTP_PROXY}
+ENV https_proxy=${HTTPS_PROXY}
+ARG DEBIAN_FRONTEND="noninteractive"
+ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
+ARG ROOT_PASSWD="root"
+ENV ROOT_PASSWD=${ROOT_PASSWD}
+ENV SSH_PORT=2222
+WORKDIR /root
+SHELL ["/bin/bash", "-c"]
+
+# base tools
+RUN <<EOT
+#!/bin/bash
+apt-get update
+apt-get install -y libgl1-mesa-glx bash-completion wget curl htop jq vim bash libaio-dev build-essential openssh-server openssh-client python3 python3-pip python3-venv bzip2 screen
+apt-get install -y --no-install-recommends software-properties-common build-essential autotools-dev nfs-common pdsh cmake g++ gcc curl wget vim tmux emacs less unzip htop iftop iotop ca-certificates openssh-client openssh-server rsync iputils-ping net-tools sudo llvm-dev re2c
+add-apt-repository ppa:git-core/ppa -y
+apt-get install -y git libnuma-dev wget
+pip install pipx
+pipx install nvitop
+pipx ensurepath 
+. ~/.bashrc
+# Configure SSH for password and public key authentication
+mkdir ~/.ssh
+# 创建或覆盖 SSH 配置文件 ~/.ssh/config
+# - Host *: 针对所有主机的通用配置
+# - ForwardAgent yes: 启用 SSH 代理转发，允许通过本地的 SSH 代理进行身份验证
+# - StrictHostKeyChecking no: 禁用主机密钥检查，自动接受新的主机密钥（适用于自动化环境）
+printf "Host * \n    ForwardAgent yes\nHost *\n    StrictHostKeyChecking no" > ~/.ssh/config
+cp /etc/ssh/sshd_config /etc/ssh/sshd_config.bak
+sed -i 's/#PermitRootLogin prohibit-password/PermitRootLogin yes/' /etc/ssh/sshd_config
+sed -i 's/#PasswordAuthentication yes/PasswordAuthentication yes/' /etc/ssh/sshd_config
+sed -i 's/#PubkeyAuthentication yes/PubkeyAuthentication yes/' /etc/ssh/sshd_config
+sed -i 's/^\(\s*\)GSSAPIAuthentication yes/\1GSSAPIAuthentication no/' /etc/ssh/ssh_config
+sed -i "s/^#Port 22/Port ${SSH_PORT}/" /etc/ssh/sshd_config
+sudo sed -i "s/#   Port 22/Port ${SSH_PORT}/" /etc/ssh/ssh_config
+ssh-keygen -t rsa -b 4096 -f /root/.ssh/id_rsa -N "" <<< y
+cat ~/.ssh/id_rsa.pub >> ~/.ssh/auth
+cat /root/.ssh/id_rsa.pub >> /root/.ssh/authorized_keys
+cat /root/.ssh/id_rsa.pub >> /root/.ssh/authorized_keys2
+chmod 600 /root/.ssh/authorized_keys
+chmod 600 /root/.ssh/authorized_keys2
+mkdir /var/run/sshd
+echo "root:${ROOT_PASSWD}" | chpasswd
+mkdir -p ~/.pip
+# install pixi
+curl -fsSL https://pixi.sh/install.sh | bash
+EOT
+
+ARG FFTW_VERSION="3.3.10"
+ENV FFTW_VERSION=${FFTW_VERSION}
+ENV PATH=/usr/local/fftw:$PATH
+# 安装fftw
+RUN <<EOT
+#!/bin/bash
+wget http://www.fftw.org/fftw-${FFTW_VERSION}.tar.gz
+tar zxvf fftw-${FFTW_VERSION}.tar.gz
+cd fftw-${FFTW_VERSION}
+./configure --prefix=/usr/local/fftw --enable-sse2 --enable-avx --enable-float --enable-avx2 --enable-shared  # 若CPU支持AVX512指令集，且有多于1个AVX512 FMA单元，则可加上--enable-avx512以进一步提升性能
+make -j$(nproc)
+make install
+EOT
+
+# 安装openmpi
+ENV MPI_HOME=/usr/local/openmpi
+ENV PATH=${MPI_HOME}/bin:/usr/bin:$PATH
+ENV LD_LIBRARY_PATH=/usr/local/cuda/lib64:${MPI_HOME}/lib:/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH
+ENV LIBRARY_PATH=/usr/local/cuda/lib64:${LIBRARY_PATH}
+ENV CPATH=/usr/local/cuda/include:${MPI_HOME}/include:${CUDA_HOME}/include:$CPATH
+# export C_INCLUDE_PATH=/usr/local/cuda/include:$C_INCLUDE_PATH
+# export LIBRARY_PATH=/usr/local/cuda/lib64:$LIBRARY_PATH
+# export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
+RUN <<EOT
+#!/bin/bash
+apt update &&  apt install -y autoconf automake libtool flex
+/usr/bin/python3 -m pip install cython
+git clone --recursive https://github.com/open-mpi/ompi.git
+cd ompi
+git checkout main
+# make clean
+# make distclean
+./autogen.pl
+mkdir build
+cd build
+../configure --with-cuda=/usr/local/cuda --enable-python-bindings --enable-mpirun-prefix-by-default --prefix=${MPI_HOME} --with-python=/usr/bin/python3
+make -j$(nproc)
+make install
+# 验证CUDA支持
+cat <<EOF > ./test_mpi_cuda.cu
+#include <mpi.h>
+#include <cuda_runtime.h>
+#include <stdio.h>
+
+__global__ void hello_cuda() {
+    printf("Hello from CUDA kernel! Thread id: %d\n", threadIdx.x);
+}
+
+int main(int argc, char **argv) {
+    MPI_Init(&argc, &argv);
+
+    int rank;
+    MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+
+    printf("Hello from MPI process %d!\n", rank);
+
+    // Launch CUDA kernel
+    hello_cuda<<<1, 10>>>();
+    cudaDeviceSynchronize();  // Wait for the CUDA kernel to finish
+
+    MPI_Finalize();
+    return 0;
+}
+EOF
+nvcc -o test_mpi_cuda test_mpi_cuda.cu -I${CUDA_HOME}/include -I${MPI_HOME}/include -L${MPI_HOME}/lib -lcudart -lmpi
+# mpirun --allow-run-as-root -np 2 ./test_mpi_cuda
+EOT
+
+# 安装plumed
+ARG PLUMED_VERSION="2.9.1"
+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:$PATH
+RUN <<EOT
+#!/bin/bash
+# git clone https://github.com/plumed/plumed2
+# cd plumed2
+# git checkout v${PLUMED_VERSION}
+curl -L -o plumed-${PLUMED_VERSION}.tar.gz https://github.com/plumed/plumed2/releases/download/v${PLUMED_VERSION}/plumed-${PLUMED_VERSION}.tgz
+tar zxvf plumed-${PLUMED_VERSION}.tar.gz
+cd plumed-${PLUMED_VERSION}
+./configure --prefix=/usr/local/plumed
+make -j$(nproc)
+make install 
+EOT
+
+# 安装gromacs
+ARG GROMACS_VERSION="2022.5"
+ENV GROMACS_VERSION=${GROMACS_VERSION}
+ENV GROMACS_HOME=/usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}
+ENV PATH=PATH=$GROMACS_HOME/bin:$PATH
+RUN <<EOT
+#!/bin/bash
+wget -c https://ftp.gromacs.org/gromacs/gromacs-${GROMACS_VERSION}.tar.gz
+tar zxvf gromacs-${GROMACS_VERSION}.tar.gz
+cd gromacs-${GROMACS_VERSION}
+### patch the plumed
+# plumed-patch -p
+plumed-patch -p -e gromacs-${GROMACS_VERSION}
+mkdir build
+cd build
+cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION} \
+         -DGMX_BUILD_OWN_FFTW=ON \
+         -DREGRESSIONTEST_DOWNLOAD=ON \
+         -DGMX_GPU=CUDA \
+         -DGMX_MPI=ON
+make -j$(nproc)
+make install 
+echo "source /usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}/bin/GMXRC.bash" >> /root/.bashrc
+EOT
+
+COPY file/Amber24.tar.bz2 file/AmberTools24.tar.bz2 /root
+
+ENV DOWNLOAD_MINICONDA="False"
+# install ambertools
+RUN <<EOT
+#!/bin/bash
+python3 -m pip install numpy scipy matplotlib
+# 解压 Amber24
+tar -xjf Amber24.tar.bz2
+# 解压 AmberTools24
+tar -xjf AmberTools24.tar.bz2
+# 清理解压后的 .tar.bz2 文件（可选）
+rm Amber24.tar.bz2 AmberTools24.tar.bz2
+EOT
+
+RUN <<EOT
+#!/bin/bash
+apt-get clean && rm -rf /var/lib/apt/lists/*
+EOT
+
+EXPOSE 2222
+
+CMD ["/usr/sbin/sshd", "-D"]
diff --git a/docker-compose.yml b/docker-compose.yml
index 212b9c5..2a55767 100755
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,60 +1,60 @@
-version: '3.8'
-
-services:
-  gromacs:
-    build: 
-      context: .
-      dockerfile: Dockerfile.gromacs
-      args: 
-        CACHEBUST: 1
-        TAG_VERSION: "12.4.1"
-        PLUMED_VERSION: "2.9.1"
-        FFTW_VERSION: "3.3.10"
-        BUILDKIT_INLINE_CACHE: 1
-    # env_file:
-    #   - .env
-    volumes:
-      - ./data:/data
-      - /dev/shm:/dev/shm
-      - /var/tmp:/var/tmp 
-      - ./script:/root/script
-    container_name: gromacs
-    pull_policy: if_not_present
-    ulimits:
-      memlock:
-        soft: -1
-        hard: -1
-    restart: unless-stopped
-    image: hotwa/gromacs:latest
-    privileged: true
-    cap_add:
-      - ALL
-      - CAP_SYS_PTRACE
-    shm_size: '64gb'
-    # devices:
-    #   - /dev/infiniband/rdma_cm
-    #   - /dev/infiniband/uverbs0
-    #   - /dev/infiniband/uverbs1
-    #   - /dev/infiniband/uverbs2
-    #   - /dev/infiniband/uverbs3
-    #   - /dev/infiniband/uverbs4
-    #   - /dev/infiniband/uverbs5
-    #   - /dev/infiniband/uverbs6
-    #   - /dev/infiniband/uverbs7
-    #   - /dev/infiniband/uverbs8
-    environment:
-      - NVIDIA_VISIBLE_DEVICES=all
-      - NVIDIA_DRIVER_CAPABILITIES=compute,utility
-      - TMPDIR=/var/tmp
-    ports:
-      - "53322:2222" 
-      # - UCX_NET_DEVICES=mlx5_0:1,mlx5_1:1,mlx5_2:1,mlx5_4:1,mlx5_5:1,mlx5_6:1,mlx5_7:1,mlx5_8:1
-    # network_mode: host
-    command: ["/usr/sbin/sshd", "-D"]
-    deploy:
-      resources:
-        reservations:
-          devices:
-            - driver: nvidia
-              count: all
-              capabilities: [gpu]
+version: '3.8'
+
+services:
+  gromacs:
+    build: 
+      context: .
+      dockerfile: Dockerfile.gromacs
+      args: 
+        CACHEBUST: 1
+        TAG_VERSION: "12.4.1"
+        PLUMED_VERSION: "2.9.1"
+        FFTW_VERSION: "3.3.10"
+        BUILDKIT_INLINE_CACHE: 1
+    # env_file:
+    #   - .env
+    volumes:
+      - ./data:/data
+      - /dev/shm:/dev/shm
+      - /var/tmp:/var/tmp 
+      - ./script:/root/script
+    container_name: gromacs
+    pull_policy: if_not_present
+    ulimits:
+      memlock:
+        soft: -1
+        hard: -1
+    restart: unless-stopped
+    image: hotwa/gromacs:latest
+    privileged: true
+    cap_add:
+      - ALL
+      - CAP_SYS_PTRACE
+    shm_size: '64gb'
+    # devices:
+    #   - /dev/infiniband/rdma_cm
+    #   - /dev/infiniband/uverbs0
+    #   - /dev/infiniband/uverbs1
+    #   - /dev/infiniband/uverbs2
+    #   - /dev/infiniband/uverbs3
+    #   - /dev/infiniband/uverbs4
+    #   - /dev/infiniband/uverbs5
+    #   - /dev/infiniband/uverbs6
+    #   - /dev/infiniband/uverbs7
+    #   - /dev/infiniband/uverbs8
+    environment:
+      - NVIDIA_VISIBLE_DEVICES=all
+      - NVIDIA_DRIVER_CAPABILITIES=compute,utility
+      - TMPDIR=/var/tmp
+    ports:
+      - "53322:2222" 
+      # - UCX_NET_DEVICES=mlx5_0:1,mlx5_1:1,mlx5_2:1,mlx5_4:1,mlx5_5:1,mlx5_6:1,mlx5_7:1,mlx5_8:1
+    # network_mode: host
+    command: ["/usr/sbin/sshd", "-D"]
+    deploy:
+      resources:
+        reservations:
+          devices:
+            - driver: nvidia
+              count: all
+              capabilities: [gpu]
diff --git a/docker-compose_lower.yml b/docker-compose_lower.yml
index 54bb632..a3b1c8a 100755
--- a/docker-compose_lower.yml
+++ b/docker-compose_lower.yml
@@ -1,57 +1,57 @@
-version: '3.8'
-
-services:
-  gromacs:
-    build: 
-      context: .
-      dockerfile: Dockerfile.lower
-      args: 
-        CACHEBUST: 1
-        TAG_VERSION: "12.4.1"
-        PLUMED_VERSION: "2.9.1"
-        FFTW_VERSION: "3.3.10"
-        BUILDKIT_INLINE_CACHE: 1
-    # env_file:
-    #   - .env
-    volumes:
-      - ./data:/data
-    container_name: gromacs
-    pull_policy: if_not_present
-    ulimits:
-      memlock:
-        soft: -1
-        hard: -1
-    restart: unless-stopped
-    image: hotwa/gromacs:l_lower
-    privileged: true
-    cap_add:
-      - ALL
-      - CAP_SYS_PTRACE
-    shm_size: '64gb'
-    # devices:
-    #   - /dev/infiniband/rdma_cm
-    #   - /dev/infiniband/uverbs0
-    #   - /dev/infiniband/uverbs1
-    #   - /dev/infiniband/uverbs2
-    #   - /dev/infiniband/uverbs3
-    #   - /dev/infiniband/uverbs4
-    #   - /dev/infiniband/uverbs5
-    #   - /dev/infiniband/uverbs6
-    #   - /dev/infiniband/uverbs7
-    #   - /dev/infiniband/uverbs8
-    environment:
-      - NVIDIA_VISIBLE_DEVICES=all
-      - NVIDIA_DRIVER_CAPABILITIES=compute,utility
-      - TMPDIR=/var/tmp
-    ports:
-      - "53322:2222" 
-      # - UCX_NET_DEVICES=mlx5_0:1,mlx5_1:1,mlx5_2:1,mlx5_4:1,mlx5_5:1,mlx5_6:1,mlx5_7:1,mlx5_8:1
-    # network_mode: host
-    command: ["/usr/sbin/sshd", "-D"]
-    deploy:
-      resources:
-        reservations:
-          devices:
-            - driver: nvidia
-              count: all
-              capabilities: [gpu]
+version: '3.8'
+
+services:
+  gromacs:
+    build: 
+      context: .
+      dockerfile: Dockerfile.lower
+      args: 
+        CACHEBUST: 1
+        TAG_VERSION: "12.4.1"
+        PLUMED_VERSION: "2.9.1"
+        FFTW_VERSION: "3.3.10"
+        BUILDKIT_INLINE_CACHE: 1
+    # env_file:
+    #   - .env
+    volumes:
+      - ./data:/data
+    container_name: gromacs
+    pull_policy: if_not_present
+    ulimits:
+      memlock:
+        soft: -1
+        hard: -1
+    restart: unless-stopped
+    image: hotwa/gromacs:l_lower
+    privileged: true
+    cap_add:
+      - ALL
+      - CAP_SYS_PTRACE
+    shm_size: '64gb'
+    # devices:
+    #   - /dev/infiniband/rdma_cm
+    #   - /dev/infiniband/uverbs0
+    #   - /dev/infiniband/uverbs1
+    #   - /dev/infiniband/uverbs2
+    #   - /dev/infiniband/uverbs3
+    #   - /dev/infiniband/uverbs4
+    #   - /dev/infiniband/uverbs5
+    #   - /dev/infiniband/uverbs6
+    #   - /dev/infiniband/uverbs7
+    #   - /dev/infiniband/uverbs8
+    environment:
+      - NVIDIA_VISIBLE_DEVICES=all
+      - NVIDIA_DRIVER_CAPABILITIES=compute,utility
+      - TMPDIR=/var/tmp
+    ports:
+      - "53322:2222" 
+      # - UCX_NET_DEVICES=mlx5_0:1,mlx5_1:1,mlx5_2:1,mlx5_4:1,mlx5_5:1,mlx5_6:1,mlx5_7:1,mlx5_8:1
+    # network_mode: host
+    command: ["/usr/sbin/sshd", "-D"]
+    deploy:
+      resources:
+        reservations:
+          devices:
+            - driver: nvidia
+              count: all
+              capabilities: [gpu]
diff --git a/docker-compose_plumed_autofep.yml b/docker-compose_plumed_autofep.yml
index 212b9c5..160fb10 100755
--- a/docker-compose_plumed_autofep.yml
+++ b/docker-compose_plumed_autofep.yml
@@ -1,60 +1,60 @@
-version: '3.8'
-
-services:
-  gromacs:
-    build: 
-      context: .
-      dockerfile: Dockerfile.gromacs
-      args: 
-        CACHEBUST: 1
-        TAG_VERSION: "12.4.1"
-        PLUMED_VERSION: "2.9.1"
-        FFTW_VERSION: "3.3.10"
-        BUILDKIT_INLINE_CACHE: 1
-    # env_file:
-    #   - .env
-    volumes:
-      - ./data:/data
-      - /dev/shm:/dev/shm
-      - /var/tmp:/var/tmp 
-      - ./script:/root/script
-    container_name: gromacs
-    pull_policy: if_not_present
-    ulimits:
-      memlock:
-        soft: -1
-        hard: -1
-    restart: unless-stopped
-    image: hotwa/gromacs:latest
-    privileged: true
-    cap_add:
-      - ALL
-      - CAP_SYS_PTRACE
-    shm_size: '64gb'
-    # devices:
-    #   - /dev/infiniband/rdma_cm
-    #   - /dev/infiniband/uverbs0
-    #   - /dev/infiniband/uverbs1
-    #   - /dev/infiniband/uverbs2
-    #   - /dev/infiniband/uverbs3
-    #   - /dev/infiniband/uverbs4
-    #   - /dev/infiniband/uverbs5
-    #   - /dev/infiniband/uverbs6
-    #   - /dev/infiniband/uverbs7
-    #   - /dev/infiniband/uverbs8
-    environment:
-      - NVIDIA_VISIBLE_DEVICES=all
-      - NVIDIA_DRIVER_CAPABILITIES=compute,utility
-      - TMPDIR=/var/tmp
-    ports:
-      - "53322:2222" 
-      # - UCX_NET_DEVICES=mlx5_0:1,mlx5_1:1,mlx5_2:1,mlx5_4:1,mlx5_5:1,mlx5_6:1,mlx5_7:1,mlx5_8:1
-    # network_mode: host
-    command: ["/usr/sbin/sshd", "-D"]
-    deploy:
-      resources:
-        reservations:
-          devices:
-            - driver: nvidia
-              count: all
-              capabilities: [gpu]
+version: '3.8'
+
+services:
+  gromacs:
+    build: 
+      context: .
+      dockerfile: Dockerfile.gromacs
+      args: 
+        CACHEBUST: 1
+        TAG_VERSION: "12.4.1"
+        PLUMED_VERSION: "2.9.2"
+        FFTW_VERSION: "3.3.10"
+        BUILDKIT_INLINE_CACHE: 1
+    # env_file:
+    #   - .env
+    volumes:
+      - ./data:/data
+      - /dev/shm:/dev/shm
+      - /var/tmp:/var/tmp 
+      - ./script:/root/script
+    container_name: gromacs
+    pull_policy: if_not_present
+    ulimits:
+      memlock:
+        soft: -1
+        hard: -1
+    restart: unless-stopped
+    image: hotwa/gromacs:latest
+    privileged: true
+    cap_add:
+      - ALL
+      - CAP_SYS_PTRACE
+    shm_size: '64gb'
+    # devices:
+    #   - /dev/infiniband/rdma_cm
+    #   - /dev/infiniband/uverbs0
+    #   - /dev/infiniband/uverbs1
+    #   - /dev/infiniband/uverbs2
+    #   - /dev/infiniband/uverbs3
+    #   - /dev/infiniband/uverbs4
+    #   - /dev/infiniband/uverbs5
+    #   - /dev/infiniband/uverbs6
+    #   - /dev/infiniband/uverbs7
+    #   - /dev/infiniband/uverbs8
+    environment:
+      - NVIDIA_VISIBLE_DEVICES=all
+      - NVIDIA_DRIVER_CAPABILITIES=compute,utility
+      - TMPDIR=/var/tmp
+    ports:
+      - "53322:2222" 
+      # - UCX_NET_DEVICES=mlx5_0:1,mlx5_1:1,mlx5_2:1,mlx5_4:1,mlx5_5:1,mlx5_6:1,mlx5_7:1,mlx5_8:1
+    # network_mode: host
+    command: ["/usr/sbin/sshd", "-D"]
+    deploy:
+      resources:
+        reservations:
+          devices:
+            - driver: nvidia
+              count: all
+              capabilities: [gpu]