Difference between revisions of "Sample traj.xyz"
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| − | A | + | A <code>traj.xyz</code> [[trajectory file]] should adhere to the following convention: |
Number_of_atoms | Number_of_atoms | ||
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Where the units for positions are Angstrom. | Where the units for positions are Angstrom. | ||
| − | At the moment velocities ''cannot'' be provided with the XYZ format, and you need to use | + | At the moment velocities ''cannot'' be provided with the XYZ format, and you need to use <code>[[estimate_velocities]] = .true.</code>; we will try to fix this in the future. If you want to provide velocities, switch to <code>[[Sample traj.gro|gro]]</code> 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: | For a 100-molecule TIP4P water system (including dummy atoms) this looks something like this: | ||
Revision as of 19:31, 18 July 2017
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
