The colors of the interface are defined by the nearest atoms : each vertex of the surface is placed on a segment defined by an atom of each group. The coloring method is then given by a function taking two atoms are argument.

Defining a new coloring function

Defining a new coloring function is not yet well interfaced. You have to edit the $(VMD_DIR)\plugins\WIN32\tcl\intersurf1.0\color_func.tcl (or $(VMD_DIR)\plugins\noarch\tcl\intersurf1.0\color_func.tcl) to add a new function (just copy/paste and modify an exemple). To make this new function available from the interface you must edit the "intersurf_gui.tcl" in the same directory.

After the following lines of code :

$ add radiobutton -value "color_from_distance" \
-label "color_from_distance" \
-variable ::NicoStuff::color_func
$ add radiobutton -value "color_white" \
-label "color_white" \
-variable ::NicoStuff::color_func

just add :

$ add radiobutton -value "your_function_name" \
-label "as_you_want" \
-variable ::NicoStuff::color_func

It will appear in the interface.

Quantitative vs Qualitative functions

If the color represents qualitative things such as type of residues, your function must return values in the range [0..16]. If it represents quantitative values such as forces or distance, you should use values in the range [17..1024], the VMD transfert function will retreive the final colors.