• A good C compiler If you are using x86 hardware GCC is fine, but for other platforms you should definitely try to use the compilers provided by the hardware manufacturer - they are usually significantly faster. GROMACS only requires a C compiler, but since the innerloops are also provided in Fortran you should definitely try to use a Fortran compiler too - it can make a factor of three difference in speed! (Not necessary on x86 machines though, for which we provide assembly loops that are even faster).
  
  
• A good Fortran 77 compiler As stated above, this is entirely optional, but it can make a huge performance difference on non-x86 platforms. You should use the compiler provided by the hardware manufacturer, not g77 which unfortunately isn't very fast.
  If you are using Linux on alpha processors you should try the Compaq compilers at www.support.compaq.com/alpha-tools/software/.
  
  
• An MPI library if you want to run in parallel. GROMACS can run on multiple processors using the MPI communication standard, which is essentially always present on supercomputers. For local workstation networks, most of us use the LAM (Local Area Multicomputer) package, but MPICH should also work fine.
  These packages were made for CentOS 4 - you probably also need the libaio dependencies:
  
  

  Centos 4 / i386

  • lam-7.0.6-5.i386.rpm
  • libaio-0.3.103-3.i386.rpm
  • libaio-devel-0.3.103-3.i386.rpm

  Centos 4 / x86_64

  • lam-7.0.6-5.x86_64.rpm
  • libaio-0.3.103-3.x86_64.rpm
  • libaio-devel-0.3.103-3.x86_64.rpm

  Centos 4 / ia64

  • lam-7.0.6-5.ia64.rpm
  • libaio-0.3.103-3.ia64.rpm
  • libaio-devel-0.3.103-3.ia64.rpm

  Source packages / tarball

  • Source RPM: lam-7.0.6-5.src.rpm
  • source tarball: lam-7.0.6.tar.gz
  
  
  
• FFTW Instead of writing our own sloppy Fourier transforms we use the free FFTW library that can be found at www.fftw.org. You must have FFTW installed before you can configure GROMACS. If you run Linux you can use the packages below. For other platforms you have to compile from source, but the GROMACS installation instructions will guide you through it.
  
  
  • fftw3-3.0.1-4.i386.rpm.
  • fftw3-devel-3.0.1-4.i386.rpm.
  • fftw3-3.0.1-4.x86_64.rpm.
  • fftw3-devel-3.0.1-4.x86_64.rpm.
  • fftw3-3.0.1-4.ia64.rpm.
  • fftw3-devel-3.0.1-4.ia64.rpm.
  • fftw3-3.0.1-4.ppc64.rpm.
  • fftw3-devel-3.0.1-4.ppc64.rpm.
  • Source RPM: fftw3-3.0.1-4.src.rpm.
  • Source tarball: fftw-3.0.1.tar.gz.
  
  
• A recent version of the GNU assembler (i.e. binutils) If you are running GROMACS on Pentium III, Athlon, or later x86 processors you absolutely want to use the assembly loops we have written. To do this, your operating system must support SSE instructions (Linux kernel 2.4), and your version of the GNU assembler must understand Intel assembly syntax.
  
  The easiest way is probably to upgrade your Linux distribution, but if you absolutely want to you can of course compile the kernel yourself. The capabilities of the GNU assembler is checked by the configuration script. If your version is too old you can compile a newer one or install our package:
  
  
  • source code: . binutils-2.16.tar.gz
  
  
• Lesstif The optional graphical user interface to the programs will be compiled automatically if Motif is present on the system. If you do not have the commercial Motif (it is not present on Linux), you can install the free Lesstif clone from www.lesstif.org instead.
  
  

Useful analysis tools

• PyMolYou can't live without Warren DeLano's masterpiece: http://www.pymol.org.
  
  
• VMD Visual Molecular Dynamics is a large and rather versatile visualization package that uses OpenGL for display. It can read the GROMACS file formats.
  
  
• gOpenMol This is a lightweight but very nice OpenGL visualization package, which also supports animation of GROMACS trajectories. Get it from the gOpenMol homepage.
  
  
• Xmgr/Grace All the analysis tools in the GROMACS package write finished graphs that you can view with Grace (formerly Xmgr). Just get it - it is the state-of-the-art graphing tool for unix!
  
  
• Rasmol This molecular graphics program displays your PDB structures on screen using X graphics (it is thus not necessary to have OpenGL), and enables you to rotate, display and colour the structure a a number of ways. Very convenient for a Quick look at a structure. The output is low quality (bitmaps), but it can generate input scripts for molscript. The derivative software "Protein Explorer" (below) might be a better alternative, but the Chime component requires windows. Rasmol works fine on Unix, you can find it here.
  
  
• Protein Explorer This is a derivative of Rasmol with more capabilities, but it requires windows. Get it here.
  
  
• Molscript This is a script-driven program form high-quality display of molecular 3D structures in both schematic and detailed representations. You can get an academic license for free from Avatar.
  
  
• WhatIF This is a program for protein structure analysis, and can be used to create input files for some of the GROMACS analysis tools. You have to get a license for this code, see the WhatIF homepage.
  
  
• DSSP This program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format. Academic licenses are available for free through the DSSP homepage. Rename the executable to dssp!
  
  

You could also check the contributions section that contains external utility programs written by our users and modifications to the Gromacs source code.