yuhongda 发表于 2015-5-3 20:37:13

安装的gromacs 5.0.4 bin 里没有g_solvate_mpi

下面是我在ubuntu14.04下的安装gromacs过程
1.安装C,C++
sudo apt-get install build-essential
1.安装FFTW
wget http://fftw.org/fftw-3.3.4.tar.gz
tar xvf fftw-3.3.4.tar.gz
cd fftw-3.3.4
./configure--enable-DFFTWF_INCLUDE_DIR--enable-shared
make
sudo make install
2.安装cmake

wget http://www.cmake.org/files/v3.2/cmake-3.2.2.tar.gz
tar xvf cmake-3.2.2.tar.gz
cd cmake-3.2.2
./configure
make
sudo make install
make --version
3.安装openmpi
wget http://www.open-mpi.org/software ... penmpi-1.8.4.tar.gz
tar xvf openmpi-1.8.4.tar.gz
cd openmpi-1.8.4
./configure
sudo make all install
sudo gedit .bashrc
加入export PATH="$PATH:/usr/local/share/openmpi/bin"
       export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib"
sudo ldconfig
4.安装cuda环境
wget http://developer.download.nvidia ... 04_7.0-28_amd64.deb
sudo dpkg -i cuda-repo-ubuntu1404_7.0-28_amd64.deb
sudo apt-get update
sudo apt-get install cuda
sudo gedit .bashrc
加入 export PATH="$PATH:/usr/local/cuda-7.0/bin"
      export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/cuda-7.0/lib64“
5.安装gromacs
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.2.tar.gz
tar xvf gromacs-5.0.2.tar.gz
cd gromacs-5.0.2
mkdir build
cd build
cmake .. -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY="/usr/local/lib/libfftw3f.so"-DFFTWF_INCLUDE_DIR="/usr/local/include/" -DGMX_MPI=on -DGMX_GPU=on
make -j4
make check
sudo make install
sudo gedit .bashrc
source /usr/local/gromacs/bin/GMXRC
sudo ldconfig

安装后,没有solvate命令,其他命令都有。请问是5.0.4不含有这个命令,还是我的安装过程除了问题
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