System Geometry Trajectories

The current implementation of the class SystemGeometryTrajectory is not very efficient but should suffice for the examples in the distribution and for calculations on small systems. Eventually it is planned that faster trajectory formats will be implemented but, in the meantime, better performance can be obtained with the classes AmberFileTrajectoryReader and AmberFileTrajectoryWriter. Instances of these classes may be employed interchangeably with instances of the class SystemGeometryTrajectory in molecular dynamics and Monte Carlo simulations. All that is necessary is to replace statements, such as:

trajectory = SystemGeometryTrajectory ( filename, owner, mode = "r/w" )

with, when reading:

trajectory = AmberTrajectoryFileReader ( filename, owner )

and, when writing:

trajectory = AmberTrajectoryFileWriter ( filename, owner )

Although reading and writing to these trajectories is faster, floating point data is stored at a lower precision and so some information is lost. In addition these classes cannot be used by algorithms that require direct (as opposed to sequential) access to the trajectory data. These algorithms include some of the reaction-path finding methods, such as SAW.

A further advantage of the AMBER file formats is that they are relatively widely recognized and so can be read by third-party programs, such as VMD.