DCD (Flexible LAMMPS trajectory)

Coordinate reader


Coordinate writer


LAMMPS can write DCD trajectories but unlike a CHARMM trajectory (which is often called a DCD, even though CHARMM itself calls them “trj”) the time unit is not fixed to be the AKMA time unit but can depend on settings in LAMMPS. The most common case for biomolecular simulations appears to be that the time step is recorded in femtoseconds (command units real in the input file) and lengths in ångströms. Other cases are unit-less Lennard-Jones time units.

This presents a problem for MDAnalysis, because it cannot autodetect the unit from the file. By default, we assume that the unit for length is the ångström and the unit for time is the femtosecond. If this is not true, then the user should supply the appropriate units in the keywords timeunit and/or lengthunit to DCDWriter and Universe (which then calls DCDReader).