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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 <maptype> <atom selection> [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 density [atomselect top "all"] -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 universally understood by every volmap map types:

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

Implicit Ligand Sampling (volmap ils command)

This command computes a map of the estimated potential of mean force (in units of k$_B$T at 300 K) of placing a weakly-interacting gas monoatomic or multiatomic ligand at every gridpoint. These results will only be valid when averaging over a large set of frames. Note that if you have a CUDA enabled GPU then your ILS calculation will run about 20 times faster than on a CPU.

Please refer to and cite:
Cohen, J., A. Arkhipov, R. Braun and K. Schulten, "Imaging the migration pathways for O$_2$, CO, NO, and Xe inside myoglobin", Biophysical Journal 91, 1844-1857, 2006.

The command syntax differs from the other volmap commands and it has its own set of options:

volmap ils molid < minmax | pbcbox > [options]

Here minmax denotes the boundaries of the grid in which the volumetric map will be computed. It is given as a list of two 3-vectors specifying the minimum and maximum coordinates of the desired volumetric data grid {{$x_{min}$ $y_{min}$ $z_{min}$} {$x_{max}$ $y_{max}$ $z_{max}$}}. If you provide the keyword pbcbox instead of the minmax coordinates then the target grid will be set to the rectangular box that encloses the PBC cell. A typical choice for the minmax parameters would be the minmax box of a subset of your system (for instance the just protein) as returned by the measure minmax command.

Based on the grid dimensions a selection that includes all atoms within the interaction cutoff distance (specified by -cutoff) is automatically chosen for the computation of the interactions.

In case your minmax box exceeds the periodic bounday box the non-overlapping parts of your map will be ill defined and a warning is printed. In this case you should consider wrapping the coordinates so that the requested grid lies in the center of the box. You can use the pbc wrap command from the PBCtool plugin for this.

In case the nonbonded interaction margin exceeds the periodic boundaries regions of your map will be based on incomplete interactions and a warning is printed. If this happens you should use the -pbc flag which automatically takes atoms of the neighboring cells into account.

Before starting the computation, the atomic radii of each atom in the molecule should be set to the corresponding CHARMM Lennard-Jones $R_\mathrm{min}/2$ parameter (in Ångström), 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 ilstools
  ILStools::readcharmmparams [list of CHARMM parameter files]
  ILStools::assigncharmmparams <molid>

The following optional arguments are understood:

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