VMD User's Guide

• distance: creates a map for which each gridpoint contains the distance between that pointand the edge of the nearest atom. In other words, each gridpoint specifies the maximumradius of a sphere cnetered at that point which does not intersect with the spheres of anyother atoms. All atoms are treated as spheres using the atoms’ VMD radii.• coulomb: creates a map of the electrostatic field of the atom selection, made by computingthe non-bonded Coulomb potential from each atom in the selection (in units of k B T/e).The coulomb map generation is optimized to take advantage of multiple processors and programmablegraphics board if they are available.• ligand: creates 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 diatomic ligand at every gridpoint. Theseresults will only be valid when averaging over a large set of frames using the -combine pmfoption. Like slowligand but uses an optimized algorithm (for example, it calculates far-awayinteractions less often). Unlike slow ligand, it can also computes many samples per gridpoint,which makes the pmf map more accurate. Please refer to and cite: Cohen, J., A. Arkhipov,R. Braun and K. Schulten, ”Imaging the migration pathways for O 2 ,CO,NO,andXeinsidemyoglobin”, Biophysical Journal 91, 1844–1857, 2006. See additional information about theligand map type below.• slowligand: Likeligand, but uses a slower and more rigorous algorithm. It is used to testthe validity of ligand under unusual conditions. See additional information about the ligandmap type below.• mask: creates a map which is set to 0 or 1 depending on whether they are within a specifiedcutoff distance (use the -cutoff argument) of any atoms in the selection. The mask map istypically used in combination with other maps in order to hide/mask data that is far from aregion of interest.• occupancy: Each grid point is set to either 0 or 1, depending on whether it contains onbeor more atoms or not. When averaged over many frames, this will provide the fractionaloccupancy of that grid point. By default, atoms are treated as spheres using the atomic radiiand a gridpoint is considered to be ”occupied” if it lies inside that sphere. Use the -pointsargument to treat atoms as points (a grid point is ”occupied” if its grid cube contains anatom’s center).The following optional arguments are understood by most volmap map types. Some argumentsmay only apply to certain map types or may have different meaning for different map types.• -allframes: Use every frame in the molecule instead of just the current one to compute thevolumetric map. The method used to combine the various trajectory frame maps can bespecified using the -combine argument. By default, volmap only uses the current frame.• -combine < avg | max | min | stdev | pmf >: Specifies the rule to use to combineframes when using the -allframes argument. These correspond to keeping the average,maximum or minimum values from the range of calculated frames. stdev will return thestandard deviation for each point over the range of frames, and pmf uses a thermal average− ln ∑ Ni e −value i/N for each point. The default is avg.116