volmap
Create volumetric map for specified coordinates; similar to grid but takes into account atomic radii. Similar to VMD volmap.
volmap filename dx dy dz <mask> [radscale <factor>] { data <existing set> | name <setname> { size <x,y,z> [center <x,y,z>] | centermask <mask> [buffer <buffer>] } } [peakcut <cutoff>] [peakfile <xyzfile>]
filename The name of the output file with the grid density.
dx, dy, dz The grid spacing (Angstroms) in the X-, Y-, and Z-dimensions, respectively
<mask> The atom selection from which to calculate the number density.
radscale <factor> Factor by which to scale radii (by division). To match the atomic radius of Oxygen used by the VMD volmap tool, a scaling factor of 1.36 should be used. Default 1.0.
data <setname> Name of existing grid data set to use.
name <setname> Name of grid set that will be created (size/center or centermask/buffer keywords).
size <x,y,z> Specify the size of the grid in the X-, Y-, and Z-dimensions. Must be used alongside the center argument.
center <x,y,z> Specify the grid center explicitly. Note, the size argument must be present in this case. Default is the origin.
centermask <mask> The mask around which the grid should be centered (via geometric center). If this is omitted and the center and size are not
specified, the default <mask> entered (see above) is used in its place.
buffer <buffer> A buffer distance, in Angstroms, by which the edges of the grid should clear every atom of the centermask (or default mask if centermask is omitted) in every direction. The default value is 3. The buffer is ignored if the center and size are specified (see below).
peakcut <cutoff> The minimum density required to consider a local maximum a ’density peak’ in the outputted peak file (default 0.05).
peakfile <xyzfile> A file in XYZ-format that contains a carbon atom centered at the grid point of every local density maximum. This file is necessary input to the spam action command.
Grid data as a volumetric map, similar to the ’volmap’ command in VMD. The density is calculated by treating each atom as a 3-dimensional Gaussian function whose standard deviation is equal to the van der Waals radius.
The density calculated is the number density averaged over the entire simulation. The grid can be specified in one of three ways:
- An existing grid data set (from e.g. bounds), specified with the data keyword.
- Via the sizes and center specified by the size and center keywords (comma-separated strings, e.g. ’20,20,20’).
- Centered on the atoms in the mask given by centermask with an additional buffer in each direction specified by buffer.