Trajectory Files

A “trajectory” generally refers to the path that molecules take through the global cell, and is a crucial file written by desmond simulations. Desmond supports writing trajectories in two formats: XTC and DTR. The latter stores more information (such as particle velocities), and is the default for a Desmond calculation. DTR trajectories are also written into a directory, instead of a single file, which can be initially confusing. This section focuses on explaining DTR trajectories written by a Desmond calculation. For information on XTC trajectories see the xtc file format.

Trajectories are stored in a set of files representing a series of “frames”, with each frame containing the positions and velocities of all the particles and pseudoparticles in the chemical system at that particular timestep. Frames can also include system characteristics such as its total energy, temperature, volume, pressure, and dimensions of the global cell.

Frame files are typically named frameXXXXXXXXX, where the numbers represent the order of the frames in the simulation. For most simulations, all frames are at the top level of the _trj directory; simulations with extremely large framesets are split into a subdirectory structure (further described below) to avoid storage limits.

timekeys

This file contains version information, the number of frames contained in each frame file, and a map into the frame files. The number of total frames in the framsest is sizeof((timekeys) - 12) / 24.

metadata

This is an instance of a frame file, but instead of time-centered data, it contains data common to all frames in a trajectory; this data includes fields like TITLE and INVMASS. Note that it is possible for the metadata file to be empty.

clickme

This file is an artifact of the need to select files in a GUI browser (such as VMD). DTR trajectories are stored as directories, but file browsers are unable to accept directories as inputs. Selecting the clickme results in the browser selecting the enclosing directory.

.ddparams

Trajectory framesets can become quite large, and at the scale of hundreds of thousands of frames, they can exceed directory file storage limits. To get around this limit, framesets can use hierarchical subdirectory structures, and the .ddparams file contains two integers describing the subdirectory system. For reasonably sized framesets, these numbers are just 0 and 0.