Gromacs下计算MMPBSA, g_mmpbsa的安装

g_mmpbsa的下载：
http://rashmikumari.github.io/g_mmpbsa/
--------compiling-Gromacs-4.5.5--------
GROMACS需要生成静态库编译
tar zxvf gmx-4.5.5.tar.gz
cd gmx-4.5.5
mkdir build
cd build
cmake ../ -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_INSTALL_PREFIX=/opt/gmx-4.5.5
make install
-------compiling-APBS-1.3--------------
g_mmpbsa目前不支持APBS-1.4,所以请下载1.2或者1.3
tar zxvf apbs-1.3-source.tar.gz
cd apbs-1.3-source/
./configure --prefix=/opt/apbs-1.3
make
make install
-------compiling-g_mmpbsa--------------
同样下载压缩包，解压后编译
./configure --with-gmx-include=/opt/gromacs-4.5.5/include --with-gmx-lib=/opt/gromacs-4.5.5/lib --with-apbs-lib=/usr/local/lib --with-apbs=/home/user/Downloads/apbs-1.3-source --prefix=/opt/g_mmpbsa
make
make install
需要注意的是apbs的编译, 如果环境变量含有ifort,它会自动选择用intel的ifort来编译，这样g_mmpbsa也应当使用ifort来编译.或者强制apbs采用gfortran等来编译。
如此以来也可以将NAMD的轨迹转换为gromacs的轨迹来计算MMPBSA。