Gromacs

Force-Field Organization

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    The different force fields should be re-organized in separate directories. A possible structure for the share/gromacs directory would be

     share/gromacs
     share/gromacs/tutor
     share/gromacs/html
     share/gromacs/force_field
     share/gromacs/force_field/gromos_XXX
     share/gromacs/force_field/encads_XXX
     share/gromacs/force_field/encadv_XXX
     share/gromacs/force_field/oplsaa_XXX
     share/gromacs/force_field/amber99_XXX
     share/gromacs/force_field/amber03_XXX
     share/gromacs/solvent
     share/gromacs/misc
    

    where the XXX represent different versions of the force fields. Each of the force field directories can also hold topologies for solvent molecules, although it would be great to put all that in rtp files instead.

    The new solvent directory would contain different equilibrated solvents for use in e.g. genbox. The directory misc would contain miscellaneous other files, like the Cool Quote database.

    Page last modified 00:21, 13 Oct 2009 by JLemkul?