Difference between revisions of "Sample traj.xyz"

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  Number_of_atoms
 
  Number_of_atoms
 
  Name_or_comment
 
  Name_or_comment
  Atom_name_1  posx posy posz
+
  Atom_name_1  posx posy posz (velx vely velz)
  Atom_name_2  posx posy posz
+
  Atom_name_2  posx posy posz (velx vely velz)
 
  ...
 
  ...
  Atom_name_nat posx posy posz
+
  Atom_name_nat posx posy posz (velx vely velz)
  
Where the units for positions are Angstrom.
+
Where the units for positions are Angstrom and the units for velocities (which are optional if you use the <code>[[estimate_velocities]] = .true.</code> option) are Angstrom/fs.
  
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 (without velocities):
 
 
For a 100-molecule TIP4P water system (including dummy atoms) this looks something like this:
 
  
 
  400
 
  400

Latest revision as of 13:11, 29 May 2019

A traj.xyz trajectory file should adhere to the following convention:

Number_of_atoms
Name_or_comment
Atom_name_1   posx posy posz (velx vely velz)
Atom_name_2   posx posy posz (velx vely velz)
...
Atom_name_nat posx posy posz (velx vely velz)

Where the units for positions are Angstrom and the units for velocities (which are optional if you use the estimate_velocities = .true. option) are Angstrom/fs.

For a 100-molecule TIP4P water system (including dummy atoms) this looks something like this (without velocities):

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