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volmap

The volmap command creates volumetric maps (3D grids containing a value at each grid point) based on the molecular data, which can then be visualized in VMD using the Isosurface and VolumeSlice representations or using the Volume coloring mode. Also note that the VolMap plugin, accessible from the VMD Extension menu, provides a graphical front-end to many of the volmap command's capabilities.

To create a volumetric map, the volmap command is run in the following way, where the atom selection specifies the atoms and molecule to include in the calculation, and where the maptype specifies the type of volumetric data to create:

  volmap <atom selection> <maptype> [optional arguments]

For example, to create a mass density map with a cell side of 0.5 Å, averaged over all frames of the top molecule, and add the volumetric data to the top molecule, on would use:

  volmap [atomselect top "all"] density -res 0.5 -weight mass -allframes \
                                                   -combine avg -mol top

The various volumetric data map types currently supported by volmap are listed as follows. Please note that when a map type description refers to an atoms radius or beta field, etc., that these values will be read directly from VMD's associated fields for that atom. In certain cases, you may want to adjust the atom selections fields (such as radius, beta, etc.) before performing the volmap analysis.

The following optional arguments are understood by most volmap map types. Some arguments may only apply to certain map types or may have different meaning for different map types.

For the ligand and slowligand map types, the various frames should be averaged using the ``pmf" combination rule, over very many frames (i.e., always use the -allframes -combine pmf options for volmap in ligand mode). Before starting the computation, the atomic radii of each atom should be set to the corresponding CHARMM Lennard-Jones Rmin/2 parameter (in Angstroms), and the beta value of each atom should be set to the CHARMM Lennard-Jones epsilon (energy well depth in kcal/mol) parameter. This can be done using VMD's VolMap plugin. Simply call in succession the following commands within the VMD console environment to use default CHARMM values for the various atoms of a molecule:

  package require volmapgui
  VolMapGUI::readcharmmparams [optional list of CHARMM parameter files]
  VolMapGUI::assigncharmmparams <molid>

The following optional arguments are understood only by the ligand and/or slowligand map types.


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