Download VMD User's Guide

• -res resolution: Sets the resolution of the final map. This means that the volume will be
subdivided into many small cubes whose side have a length of resolution. The computation should be performed on a finer grid (see -subres option) but at the end the map is
downsampled to this resolution. A good choice for the grid resolution 1 Å (argument -res).
Lower resolutions make it difficult to see features, higher ones will be very costly in terms of
computation time. Also, since the fluctuation of the protein backbone is on the order of 1-2
Angstrom a higher grid resolution doesn’t make much sense.
• -subres num: Number of points in each dimension of the subsampling grid, e.g. 2 for a
2x2x2 subgrid or 3 for a 3x3x3 subgrid. A value of 1 means is no subsampling, the default is
(-subres 3). Without subsampling the probe is placed at each grid cell center (for diatomic
probes in numconf different random orientations, see argument -conf). This position is
assumed to be representative for the interaction of the probe in this voxel with the system.
However, for a typical voxel size of 1x1x1 Å the energy value can differ significantly within
the voxel and the value at the center might not be close to the average. Subsampling averages
over the interaction on a regular subgrid in each voxel thus producing a more accurate free
energy value for placing the probe into each voxel. Even though this severely increases the
computational cost it is highly recommended that you use subsampling! A 3x3x3 subgrid for
a 1 Å resolution map is a good choice.
• -T temperature: The temperature in Kelvin at which the MD simulation was performed.
(default: 300)
• -probesel selection: Atom selection that defines the probe molecule. The radius and occupancy fields should be populated with the VDW radii and VDW epsilon parameters from the
force field (see option -probevdw). Alternatively, you can specify the probe coordinates and
VDW parameters probe atoms directly using the -probecoor and -probevdw options.
• -probecoor atomcoords: Set the coordinates of the probe atoms in form of a list of triples
{{x0 y0 z0 } . . . {xN yN zN }}.
• -probevdw parameterlist: Set the tuple of van der Waals parameters for each probe atom
in the form {{0 Rmin,0 /2} . . . {N Rmin,N /2}}. They define the nonbonded interactions of
the probe evaluated by the Lennard-Jones potential
UVDW

Rij
ij 
=
rij
atoms i,j
X
!12
−2
Rij
rij
!6 

(9.2)
√
where Rij = (Rmin,i + Rmin,j )/2 and ij = i · j . (That’s the same form as in CHARMM
and AMBER parameter files). Units of are kcal/mol, and of R min /2 are Ångström.
• -orient n: Control the number of samples of different probe orientations for multiatom probes
at each grid point. The number n determines the angular spacing of probe orientation vectors
and of the rotations around each of these vectors.
n = 1:
n = 2:
n = 3:
n = 4:
use
use
use
use
1 orientation only
6 orientations (vertices of a octahedron)
8 orientations (vertices of a hexahedron)
12 orientations (faces of a dodecahedron)
130