Difference between revisions of "Sample traj.gro"
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lx ly lz | lx ly lz | ||
| − | Where the units for positions are nm and for velocities nm/ps. lx, ly and lz are the orthorhombic cell vectors. Velocities are optional if one uses the [[estimate_velocities]] keyword. | + | Where the units for positions are nm and for velocities nm/ps. lx, ly and lz are the orthorhombic cell vectors. DoSPT does ''not'' use these cell dimensions, use the [[cell]] keyword instead. Velocities are optional if one uses the [[estimate_velocities]] keyword. |
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 13:30, 17 July 2017
A "traj.gro" trajectory file should adhere to the following convention:
Name_or_comment Number_of_atoms Molecule_name_1 Atom_name_1 Atom_number_1 posx posy posz (velx vely velz) Molecule_name_1 Atom_name_2 Atom_number_2 posx posy posz (velx vely velz) ... Molecule_name_nmol Atom_name_nat Atom_number_nat posx posy posz (velx vely velz) lx ly lz
Where the units for positions are nm and for velocities nm/ps. lx, ly and lz are the orthorhombic cell vectors. DoSPT does not use these cell dimensions, use the cell keyword instead. Velocities are optional if one uses the estimate_velocities keyword.
For a 100-molecule TIP4P water system (including dummy atoms) this looks something like this:
Water
400
1SOL OW 1 0.750 0.843 0.511 0.3663 0.3392 -0.1709
1SOL HW1 2 0.676 0.830 0.453 -0.9593 -0.1360 1.5834
1SOL HW2 3 0.796 0.919 0.476 -0.0189 -0.3408 -2.2009
1SOL MW 4 0.747 0.851 0.499 0.1473 0.1912 -0.2062
2SOL OW 5 0.595 0.422 0.007 0.0358 0.1983 0.0845
2SOL HW1 6 0.669 0.482 0.012 0.5083 -0.3639 -0.0434
2SOL HW2 7 0.618 0.363 -0.065 -0.2093 -0.4100 0.5036
2SOL MW 8 0.608 0.422 -0.002 0.0649 0.0485 0.1217
.
.
.
100SOL OW 397 0.270 0.823 0.453 0.8555 0.6402 -0.0329
100SOL HW1 398 0.247 0.754 0.391 0.8687 0.3583 0.2780
100SOL HW2 399 0.192 0.835 0.507 1.7382 -0.9998 1.6631
100SOL MW 400 0.257 0.816 0.452 0.9702 0.3942 0.2240
1.47200 1.47200 1.47200
