Tcl scripts are used to read and represent in VMD scalar pairwise interactions; there is no representation for vector pairwise interactions.
Per-atom data is loaded into the “user” field that each atom has assigned in VMD; this field can be used to set the color of the atom. An animation can be produced by updating the value in this field for each frame, showing the variations in per-atom data as they vary in time. To load and use the pf_loaduser plugin, follow the syntax:
package require pf_loaduser
pf_loaduser <filename.psa> <residues_renumbered> <ignore_zeros> <color_scale> <color_min> <color_max>
The first line will instruct VMD to load the pf_loaduser plugin which will make available the pf_loaduser function which is called on the 2nd line. The pf_loaduser function takes several arguments:
filename.psa is a string representing the name of the file containing per-atom data; it assumes that there are as many lines with data in the file as there are currently loaded frames. There is no default, a file name should always be provided. residues_renumbered is a string containing “true” or “false”. It should correspond to whether a residue renumbering has been done (automatically or enforced) in the GROMACS PF2 code. The default is “false”. ignore_zeros is an integer; if set to 0, zeros will be taken into consideration when calculating the minimum values, if set to something else, zeros will not be taken into consideration when calculating minimum values. The default is 0. This is useful for the case when analyzing only a subset of atoms in which case the atoms not analyzed will have a zero value. If color_min is given, ignore_zeros will not have any effect. color_scale is a string representing the name of the VMD color scale. The default is “BGR”. color_min and color_max are floating point numbers representing the minimum and maximum values used for color mapping, useful when doing a uniform mapping for several trajectories; if they are not specified or specified as “-1”, the minimum and maximum values found in the file will be used.
At the end of loading a per-atom/per-residue data file, the Tcl script will print the minimum and maximum values used for color mapping. Example for using the pf_loaduser plugin: load a PDB file and a trajectory then at the console or in the Tk console type:
package require pf_loaduser
animate delete beg 0 end 0 skip 0 0
pf_loaduser "peratom-sum.psa"
The second line tells VMD to remove the first frame – this is needed as the PDB will act as the first frame and the .psa file contains only as many frames as there are in the trajectory. The third line loads the user data from the “peratom-sum.psa” file and lets VMD automatically map the colors using the minimum and maximum value from this file.
As the data is assigned to the per-atom “user” field, VMD takes care of updating the colors when drawing each frame. For residue-based data, all atoms in a residue receive the same per-atom “user” data.
Scalar pairwise forces are represented as a set of cylinders drawn for each pair between the coordinates of the 2 atoms. The scalar values are mapped to either thickness or color of cylinders. To load and use the pf_draw plugin, follow the syntax:
package require pf_draw
pf_init <max_cylinder_width> <what_to_scale>
pf_read <filename.pfa> <residues_renumbered>
pf_draw
The first line will instruct VMD to load the pf_draw plugin which will make available functions shown on the 2nd to 4th line. The second line initializes the plugin: max_cylinder_width is a floating point number specifying the maximum cylinder width; what_to_scale is either “cyl_w” - scale width or “cyl_col” - scale color. The third line reads scalar pairwise force data (as output with atombased set to scalar) from the specified file; residues_renumbered is a string containing “true” or “false” and should correspond to whether a residue renumbering has been done (automatically or enforced) in the GROMACS PF2 code - the default is “false”. The fourth line draws the cylinders for the currently active structure (a PDB file or the last frame of a trajectory); any cylinders drawn previously are removed before drawing new ones. When scaling the cylinder width, the maximum cylinder width is taken from the pf_init command line. For each pair of atoms, the value used as cylinder width is the absolute value of the pairwise force. To show the sign of the pairwise forces, the cylinders are colored red for positive pairwise forces and blue for negative ones (zero forces can't be visualized as the cylinder width would be zero). When scaling the cylinder color, the cylinder width is taken from the pf_init command line. For each pair of atoms, the value used as cylinder color is the value of the pairwise force scaled such that the minimum pairwise force corresponds to the lowest color, the maximum pairwise force corresponds to the maximum color and a zero pairwise force corresponds to the midpoint of the color scale. At the end of reading a scalar pairwise forces file, the Tcl script will print the difference between the maximum and minimum force in the set; this difference is used for color scaling. Example for using the pf_loaduser plugin: load a PDB file and a trajectory then at the console or in the Tk console type:
package require pf_draw
animate delete beg 0 end 0 skip 0 0
pf_init 0.2 "cyl_w"
pf_read "summed_scalar.pfa"
trace variable vmd_frame(0) w pf_draw
The second line tells VMD to remove the first frame – this is needed as the PDB will act as the first frame and the .pfa file contains only as many frames as there are in the trajectory. The third line will initialize the drawing to scale by cylinder width, with a maximum cylinder width of 0.2 – this value needs experimentation. The fifth line looks a bit strange – it tells VMD to call the function pf_draw for each drawing of a frame; this is needed because VMD doesn't know what to do with the pairwise forces values. If this line would be replaced by a simple pf_draw, cylinders would be drawn for the currently loaded PDB file or last frame of the trajectory but they would not be updated when VMD displays a different frame. If there are many pairwise forces to be represented, drawing the cylinders from a Tcl function can become slow and the display can become cluttered with so many geometrical shapes. It's recommended to filter the pairwise forces, so that only a few are represented at a time.
Ensure that vmd is in your PATH, change into tests/alagly and execute:
vmd -e pairwise_forces_scalar_summed_atom.vmd
vmd -e pairwise_forces_scalar_summed_residue.vmd
vmd -e stress_atom.vmd
vmd -e stress_residue.vmd