A Julia package for reading and writing molecular dynamics simulation trajectories.
Currently supports iteration over a series of GROMACS-format .gro files and
writing of a single trajectory frame as a .gro file.
GROMACS-format .xtc files will be supported in a future release.
julia> using MolecularTrajectories
julia> using StaticArrays
julia> const Vec = SVector{3, Float64}
julia> gro_path = joinpath(dirname(pathof(MolecularTrajectories)), "../test/test.gro")
julia> gro_paths = [gro_path, gro_path]
julia> trajectory = GroTrajectory{Vec}(gro_paths, dt=1.0)
julia> for frame in trajectory
@show frame.time
@show frame.box
@show frame.positions[1:10]
@show frame.velocities[1:10]
end
julia> using MolecularTopologies
julia> topology = open(gro_topology, gro_path)
julia> frame = first(GroTrajectory{Vec}(gro_paths, dt=1.0))
julia> open("output.gro", "w") do g
write_frame(g, GroTrajectory, frame, topology, "Some gro file")
end
Note that trajectory objects are iterable but not indexable;
they do not support the AbstractArray interface.