Sample traj.gro

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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