Difference between revisions of "Sample traj.gro"
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| − | A | + | A <code>traj.gro</code> [[trajectory file]] should adhere to the following convention: |
Name_or_comment | Name_or_comment | ||
| Line 9: | Line 9: | ||
lx ly lz | lx ly lz | ||
| − | Where 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. <code>lx</code>, <code>ly</code> and <code>lz</code> are the orthorhombic cell vectors. DoSPT does ''not'' use these cell dimensions, use the <code>[[cell]]</code> keyword instead. Velocities are optional if one uses the <code>[[estimate_velocities]]</code> keyword. |
| + | |||
| + | Note that, although native Gromacs trajectory files are "fixed format", we accept any floats which appear in the same order as in the original files. That is, you do not need to adhere to the precision convention for Gromacs as long as you provide the correct number of input elements in the correct order. | ||
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: | ||
Latest revision as of 19:36, 18 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.
Note that, although native Gromacs trajectory files are "fixed format", we accept any floats which appear in the same order as in the original files. That is, you do not need to adhere to the precision convention for Gromacs as long as you provide the correct number of input elements in the correct order.
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
