Sample traj.xyz - Revision history

Miguel Caro at 13:11, 29 May 2019

2019-05-29T13:11:47Z

Miguel Caro at 19:31, 18 July 2017

2017-07-18T19:31:47Z

Miguel Caro: 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 ......"

2017-07-17T13:28:40Z

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 ......"

New page

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 [[Sample traj.gro|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

@@ Line 3: / Line 3: @@
   Number_of_atoms
   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):

@@ Line 1: / Line 1: @@
-A "traj.xyz" [[trajectory file]] should adhere to the following convention:
+A <code>traj.xyz</code> [[trajectory file]] should adhere to the following convention:
   Number_of_atoms
@@ Line 10: / Line 10: @@
 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 [[Sample traj.gro|gro]] format for the time being (note different units and format conventions).
+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: