The biggest improvement in VMD 1.1 has been the addition of commands for analyzing atomic and molecular information. This chapter describes through examples how to put those commands together to write scripts. We assume at this point you already read through the other chapters which describe the various commands, including:
The examples used will not be described in detail, but will only
explain some of the more unusual or novel features of the VMD
scripting language. The source of the examples can be found
in the VMD script library at
Many of these scripts use the trace command from Tcl. This does not mean all good scripts must use that command, but rather that putting a trace on a variable is a nice way to add an automatic action.