GROMACS requires an ANSI C compiler that complies with the C89 standard. For best performance, the GROMACS team strongly recommends you get the most recent version of your preferred compiler for your platform (e.g. GCC 4.7 or Intel 12.0 or newer on x86 hardware). There is a large amount of GROMACS code introduced in version 4.6 that depends on effective compiler optimization to get high performance - the old assembly-language routines have all gone. For other platforms, use the vendor's compiler, and check for specialized information below.

I am new to install Gromacs in windows 7, i encountered with a problem when installed fftw-3.3.4 in cygwin (64-bit). The returned result showed 'no such directory or file' from the bash when i typed in './configure.' .The folder (directory of fftw is C:/). In bioinformatics, GROMACS is one of the most popular Molecular Dynamics simulation software with a load of features built in. Installing GROMACS Version 5.x.x+ can be a tedious and cumbersome process on Ubuntu, especially if you are just starting out.

It is important to examine how you will use GROMACS and upon what hardware and with what compilers in deciding which parallelization paths to make available. Testing the performance of different options is unfortunately mandatory. The days of being able to just build and run ' mdrun' and get decent performance by default on your hardware are long gone.

GROMACS will always run correctly, and does a decent job of trying to maximize your performance, but if you want to approach close to the optimum, you will need to do some work for it! If you build FFTW from source yourself, get the most recent version and follow its installation guide (e.g. Choose the precision (i.e.

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Single or float vs double) to match what you will later require for GROMACS. There is no need to compile with threading or MPI support, but it does no harm.

On x86 hardware, compile only with --enable-sse2 (regardless of precision) even if your processors can take advantage of AVX extensions to SSE. The way GROMACS uses Fourier transforms cannot take advantage of this feature in FFTW because of memory system performance limitations, it can degrade performance by around 20%, and there is no way for GROMACS to require the use of the SSE2 at run time if AVX support has been compiled into FFTW. The best way to use CMake to configure GROMACS is to do an “out-of-source” build, by making another directory from which you will run CMake. This can be a subdirectory or not, it doesn't matter. It also means you can never corrupt your source code by trying to build it! So, the only required argument on the CMake command line is the name of the directory containing the CMakeLists.txt file of the code you want to build.

For example, download the source tarball and use $ tar xfz gromacs-4.6-beta1-src.tgz $ cd gromacs-4.6-beta1 $ mkdir build-cmake $ cd build-cmake $ cmake. CMake works in an iterative fashion, re-running each time a setting is changed to try to make sure other things are consistent. Once things seem consistent, the iterations stop. Once cmake returns, you can see all the settings that were chosen and information about them by using $ ccmake. Check out for general advice on what you are seeing and how to navigate and change things. The settings you might normally want to change are already presented. If you make any changes, then ccmake will notice that and require that you re-configure (using ' c'), so that it gets a chance to make changes that depend on yours and perform more checking.

This might require several configuration stages when you are using ccmake - when you are using cmake the iteration is done behind the scenes. Once you become comfortable with setting and changing options, you may know in advance how you will configure GROMACS.

If so, you can speed things up by invoking cmake with a command like: $ cmake. -DGMX_GPU=ON -DGMX_MPI=ON -DGMX_INSTALL_PREFIX=/home/marydoe/programs to build with GPUs, MPI and install in a custom location. You can even save that in a shell script to make it even easier next time. You can also do this kind of thing with ccmake, but you should avoid this, because the options set with ' -D' will not be able to be changed interactively in that run of ccmake. We'd like users to have the ability to change any setting and still have the CMake cache stable; ie. Not have things you set mysteriously change, or (worse) the whole thing breaks.