The trajectory file contains the most important input information to carry out a DoSPT calculation: atomic positions and velocities. Ideally, the trajectory file will contain synchronous positions and velocities, but one must be aware of the fact that some MD integrators, for instance leap-frog, will use positions and velocities which are offset by half an MD time step. Such information cannot be used to obtain angular momenta and one must thus discard either the velocities or the positions. In other cases, some of the information may be missing from the trajectory file, for instance it is common that only the positions are contained in the trajectory file. In both cases, asynchronous velocities/positions and missing velocities, the
estimate_velocities keyword can be used to force DoSPT to estimate the velocities by interpolating from the positions. One must note however that such interpolation will yield a bad estimate of velocities if the saving time step (which is equal or larger than the integration time step) is too large.
Currently, DoSPT only supports ASCII (i.e., text-based) trajectory files. We are aware that reading binary trajectory files is much more efficient time-wise. Eventually, support for reading-in binary trajectory files will be added to the code. Until then, you must use one of the following formats and include the corresponding
format keyword in your
||File name convention||What this format looks like||Comments|
|Gromacs||gro||traj.gro||sample traj.gro||Although native Gromacs trajectory files are "fixed format", we accept any floats which appear in the same order as in the original files. That is, you do not need to adhere to the precision convention for Gromacs as long as you provide the correct number of input elements in the correct order.|
|XYZ||xyz||traj.xyz||sample traj.xyz|| There is no universally accepted XYZ format. The convention we use corresponds to the most commonly found XYZ format. Note that currently DoSPT cannot read velocities from xyz files (only positions). Therefore, at the moment xyz files must be used in conjunction with |