Gromacs 4.0.7并行带QM/MM安装
平台
SUSE Linux Enterprise Desktop 10 SP3
gcc4.1.2
mpich2-1.2.1p1
ifrot 10.1
fftw 3.2.2

解压缩mpich2-1.2.1p1.tar.gz进入此目录，运行：
./configure
make        
make install

运行
touch /etc/mpd.conf         
chmod 700 /etc/mpd.conf
将下面加入mpd.conf:
secretword=<secretword>            (比如secretword=ltwd)

解压fftw3.2.2压缩后进入目录，安装到/soft/fftw下
./configure --enable-float --enable-threads
make
make install
把libmopac.a复制到/soft/fftw/lib和/lib下
配置环境变量
setenv CPPFLAGS -I/soft/fftw/include
setenv LDFLAGS -L/soft/fftw/lib

解压gromacs4.0.7，进入目录
./configure --prefix=/soft/gromacs --enable-mpi -enable-fortran --with-qmmm-mopac --enable-shared
make
make install
配置环境变量
setenv LIBS -lmopac
setenv LD_LIBRARY_PATH /soft/gromacs/lib
source /soft/gromacs/bin/completion.csh
set path=(/soft/gromacs/bin $path)



configure中的其他选项

CC          C compiler command     一般这个环境变量就是gcc
CFLAGS      C compiler flags      编译时的参数，一般是-O3
LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries in a
              nonstandard directory <lib dir>           库文件目录
LIBS        libraries to pass to the linker, e.g. -l<library>          设的时候不用“-l xxx”，无需引号
CPPFLAGS    C/C++/Objective C preprocessor flags, e.g. -I<include dir> if
              you have headers in a nonstandard directory <include dir>
F77         Fortran 77 compiler command    一般这个环境变量就是gfortran或ifort
FFLAGS      Fortran 77 compiler flags     编译时的参数，一般是-O3
CCAS        assembler compiler command (defaults to CC)
CCASFLAGS   assembler compiler flags (defaults to CFLAGS)
CPP         C preprocessor
CXX         C++ compiler command      一般是g++
CXXFLAGS    C++ compiler flags
CXXCPP      C++ preprocessor
XMKMF       Path to xmkmf, Makefile generator for X Window System


Optional Features:
--disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
--enable-FEATURE[=ARG] include FEATURE [ARG=yes]
--enable-shared[=PKGS] build shared libraries [default=no]
--disable-float               use double instead of single precision
--enable-double               same effect as --disable-float
--enable-fortran              use fortran (default on sgi,ibm,sun,axp)
--enable-mpi                  compile for parallel runs using MPI
--disable-threads             don't try to use multithreading
--enable-mpi-environment=VAR only start parallel runs when VAR is set
--disable-ia32-3dnow          don't build 3DNow! assembly loops on ia32
--disable-ia32-sse            don't build SSE/SSE2 assembly loops on ia32
--disable-x86-64-sse           don't build SSE assembly loops on X86_64
--disable-ppc-altivec         don't build Altivec loops on PowerPC
--disable-ia64-asm            don't build assembly loops on ia64
--disable-cpu-optimization    no detection or tuning flags for cpu version
--disable-software-sqrt       no software 1/sqrt (disabled on sgi,ibm,ia64)
--enable-prefetch-forces      prefetch forces in innerloops
--enable-all-static           make completely static binaries
--disable-dependency-tracking speeds up one-time build
--enable-dependency-tracking   do not reject slow dependency extractors
--enable-static[=PKGS] build static libraries [default=yes]
--enable-fast-install[=PKGS]
                          optimize for fast installation [default=yes]
--disable-libtool-lock avoid locking (might break parallel builds)
--disable-largefile     omit support for large files

Optional Packages:
--with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
--without-PACKAGE       do not use PACKAGE (same as --with-PACKAGE=no)
--with-fft=[fftw3/fftw2/mkl(>=6.0)/fftpack]
                          FFT library to use. fftw3 is default, fftpack built
                          in.
--with-external-blas    Use system BLAS library (add to LIBS). Automatic on
                          OS X.
--with-external-lapack Use system LAPACK library (add to LIBS). Automatic
                          on OS X.
--without-qmmm-gaussian Interface to mod. Gaussian0x for QM-MM (see website)
--with-qmmm-gamess      use modified Gamess-UK for QM-MM (see website)
--with-qmmm-mopac       use modified Mopac 7 for QM-MM (see website)
--with-gnu-ld           assume the C compiler uses GNU ld [default=no]
--with-pic              try to use only PIC/non-PIC objects [default=use
                          both]
--with-tags[=TAGS]      include additional configurations [automatic]
--with-dmalloc          use dmalloc, as in
     http://www.dmalloc.com/dmalloc.tar.gz
--with-x                use the X Window System
--with-motif-includes=DIR     Motif include files are in DIR
--with-motif-libraries=DIR    Motif libraries are in DIR
--without-gsl                 do not link to the GNU scientific library, prevents certain analysis tools from being built
--with-xml                    Link to the xml2 library, experimental

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