Wednesday, March 23, 2011

Installing Gromacs 4.0.x on CentOS 5.x

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers

Do note that this Gromacs Installation Guide is for Gromacs 4.0.x. For detailed instruction, see GROMACS Installation Instructions. For installation of FFTW, you may want to take a look at Blogh Entry Installing FFTW

Since I'm using FFTWMPI (OpenMPI to be exact) and configure FFTW with --prefix=/usr/local/fftw,

I've configured the following

# ./configure CPPFLAGS="-I/usr/local/fftw/include" LDFLAGS="-L/usr/local/fftw/lib" \ 
--with-fft=fftw3 --enable-mpi --disable-float
Some notes...... (Assuming you are using bash)

  1. CPPFLAGS="-I/usr/local/fftw/include"
  2. LDFLAGS="-L/usr/local/fftw/lib"
  3. To compile with FFTW version 3 "--with-fft=fftw3"
  4. To enable MPI "--enable-mpi"
  5. To select Double precision  "--disable-float"
# make -j 8
where 8 is the number of cores.

# make mdrun
* if you have configure with "--enable-mpi"
# make install
* Install all the binaries, libraries and shared data files with:
# make install-mdrun
* If you only want to build the mdrun executable (in the case of an MPI build),

# make links
* If you want to create links in /usr/local/bin to the installed GROMACS executables

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