Using VMD plugins to read trajectory formats not native to GROMACS

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    If a VMD (>=1.8.6) installation exists and your machine supports dynamic loading, all GROMACS tools since version 4.0.7 have the ability to read any trajectory file format that can be read by the VMD installation (e.g. AMBER's DCD format). The VMD_PLUGIN_PATH environment variable can be set to point to the molfile folder within the VMD installation, which might be found automatically if your VMD is installed in the standard location. If so, any GROMACS tool will accept file.dcd instead of file.trr, for example.

    Once GROMACS 4.6 is available, CMake will be able to detect VMD and determine whether plugins can be used. There will not be a need to set an environment variable at run time, however VMDDIR and VMD_PLUGIN_PATH environment variables will be available to point to new VMD installations and/or their molfile folders, respectively, should the need arise. Gromacs and VMD need to be compile both for 32 bit or both for 64 bit.

    There is no ability for GROMACS tools to write files using the VMD plugins.

    Page last modified 04:13, 26 Apr 2013 by rolandschulz