load_traj reads trajectory files (currently just AMBER files). The file extension is used to determine the format. AMBER files must end in ".trj"
In newer builds of PyMOL (namely, version 1.0 or newer), several additional formats are accepted. CHARMM trajectories (".dcd") are also valid files and only require a structure to be loaded first while the trajectory file gets loaded as sequential states into the associated object.
load_traj filename [,object [,state [,format [,interval [,average ] [,start [,stop [,max [,selection [,image [,shift ]]]]]]]]]
cmd.load_traj(filename,object='',state=0,format='',interval=1, average=1,start=1,stop=-1,max=-1,selection='all',image=1, shift="[0.0,0.0,0.0]")
You must first load a corresponding topology file before attempting to load a trajectory file.
PyMOL does not know how to wrap the truncated octahedron used by Amber You will need to use the "ptraj" program first to do this.
The average option is not a running average. To perform this type of average, use the "smooth" command after loading the trajectory file.