Sample traj.xyz
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Revision as of 13:28, 17 July 2017 by Miguel Caro (talk | contribs) (Created page with "A "traj.xyz" trajectory file should adhere to the following convention: Number_of_atoms Name_or_comment Atom_name_1 posx posy posz Atom_name_2 posx posy posz ......")
A "traj.xyz" trajectory file should adhere to the following convention:
Number_of_atoms Name_or_comment Atom_name_1 posx posy posz Atom_name_2 posx posy posz ... Atom_name_nat posx posy posz
Where the units for positions are Angstrom.
At the moment velocities cannot be provided with the XYZ format, and you need to use "estimate_velocities = .true."; we will try to fix this in the future. If you want to provide velocities, switch to gro format for the time being (note different units and format conventions).
For a 100-molecule TIP4P water system (including dummy atoms) this looks something like this:
400 Water OW 7.50 8.43 5.11 HW1 6.76 8.30 4.53 HW2 7.96 9.19 4.76 MW 7.47 8.51 4.99 OW 5.95 4.22 0.07 HW1 6.69 4.82 0.12 HW2 6.18 3.63 -0.65 MW 6.08 4.22 -0.02 . . . OW 2.70 8.23 4.53 HW1 2.47 7.54 3.91 HW2 1.92 8.35 5.07 MW 2.57 8.16 4.52
