Gromacs

Installation Instructions 4.5

    Version as of 04:47, 19 Oct 2019

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    Full details on how to install GROMACS are provided here: Installation Instructions. Here we give a quick and dirty installation guide as well.

    To remove a GROMACS installation, see Removing Installation.

     

    Using MPI
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    You may notice that the above instructions for an MPI installation (so you can run in parallel) recommend only doing make mdrun and make install-mdrun. That's because in GROMACS version 3.x, only mdrun is MPI-aware. In GROMACS 4.x, some of the utility programs are also MPI-aware, but these will only be for compute-intensive utilities (e.g. that diagonalize large matrices, or calculate autocorrelations, etc.). Building and installing the other utilities with configure --enable-mpi is a waste of time, as is attempting to use any resulting MPI-linked-but-unaware utilities with mpirun.

    Test Set
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    A test set is available for testing of a GROMACS installation.

    Getting access to GROMACS after installation
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    In a normal Unix/Linux/Cygwin/MacOS environment you will need to know the location where GROMACS is installed, e.g.

    /usr/local/gromacs

    . In your shell configuration file (e.g.

    .bashrc

    for

    bash

    or

    .cshrc

    /

    .tcshrc

    for

    tcsh

    ) you should use a command analogous to

    source /usr/local/gromacs/bin/GMXRC

    near the end of that file.

    GMXRC

    then magically determines the type of shell you are using and configures your

    PATH

    ,

    MANPATH

    ,

    GMXDATA

    etc.

    environment variables

    so that GROMACS works as intended. Note that you will then need to re-source your shell configuration file, or open a new shell in order to have the intended effect. If you prefer, you can interactively invoke the

    source

    command as above from your command line, and if you know you might want access to multiple versions of GROMACS in an interchangeable manner, this can be a useful approach.

    At some larger computing facilities, you should consult their documentation and/or staff for instructions on how GROMACS was installed and how you should get access to it and use it.

    Just as with everything else in the UNIX world, you should not do your daily work with GROMACS as root or superuser. It's unnecessary and highly risky. See here for more information.

    Having difficulty?
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    If you encounter a problem with installing GROMACS, then there are a number of locations where you can find assistance. It is recommended that you follow these steps to find the solution:

    1. read the installation instructions again, taking note that you have followed each and every step correctly.
    2. search the GROMACS website and users emailing list for information on the error.
    3. search this wiki for information.
    4. search the internet using a search engine such as Google.
    5. post to the GROMACS users emailing list for assistance.

    Specialty Instructions
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    Page last modified 15:41, 14 Sep 2009 by rossen