%command          # 1
   %%                # 2
   include filename  # 3
#
   dynamics dyn      # 4
   minimize min      # 5
   monte_carlo mon   # 6
#
   archive           # 7
   update_list       # 8
   backup            # 9
   restore           # 10
   center            # 11
   energies          # 12

The first two commands are for programming support:. (1) Run the shell command now. (2) Execute the commands assembled up to this point now. (3) Inset filename at this point as part of this script; typically used to insert a macro definition (see below).

(4) Run dyn steps of molecular dynamics. (5) Run min steps of energy minimization. (6) Run mon cycles of monte carlo each cycle consisting of as many attempted moves as there are atoms. The runs of these three simulation methods are carried out using the current settings or preset values if no settings have been made; these setttings can be modified (see below).

(7) Write to the output archive file; whether it is coordinates and/or velocities depends on the settings (see modify environment). (8) Update the non-bond lists now; normally this is done periodically in each of the simulation methods and the intervals between updates can be set. (9) Make a backup copy of the current coordinates in memory. (10) Restore the coordinates previously saved in memory. (11) Center the entire system on the origin. (12) Calculate and print the energies now.

The modification commands (below) can contain as many keyword-value pairs as you like; new pairs overwrite previous values. Modifications can be done as many time as needed; typically these are interspersed with simulation commands and other modification commands. There are preset values for all keywords, listed in the comments below.