DCD (Flexible LAMMPS trajectory)¶
Coordinate reader |
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Coordinate writer |
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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).