Trajectories¶

The main output of a molecular simulation is often a series of conformations of a molecular system, as successively produced by the software over time.

Example applications that produce such a trajectory are molecular dynamics (MD) simulations, and geometry optimizations.

The conformations consist of coordinates for all the atoms in the system, and - depending on the format - information on its periodicity, atomic elements and the location of covalent bonds.

Some file formats include

• XYZ format (xyz), which is a human readable format that stores elements and coordinates for every conformation.

• Compact binary DCD format (dcd), which stores only coordinates and periodic lattice vectors,

• Binary RKF format (rkf) which is the native format of the Amsterdam Modeling Suite, and is able to store any desired information on the system.

• Binary .traj (traj) format, which is the native format used by the Atomic Simulation Environment

For trajectory conversion tools, see File format conversion tools

PLAMS provides the possibility to analyze and alter single conformations of a molecular system through the Molecule object .

The trajectories module provides the possibility to extract such a conformation from a trajectory file and load it into a Molecule object, as well as write (altered) conformations to a new trajectory file of one in the three formats described above.