Generating trajectories of Gromacs PCA's

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This is a suggestion for a mdanalysis improvement: to be able to generate 
trajectories of Gromacs PCA's. 

PCA are trr files without forces and velocities (only positions, which 
represent PCA vectors). The mode index is numbered in "step".

These are the first few lines of gmxdump -f pca.trr...

   natoms=      1252  step=         1  time=3.2866406e+00  lambda=         0
   box (3x3):
      box[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      box[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      box[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   x (1252x3):
      x[    0]={ 2.32158e-02,  1.46866e-03, -7.98529e-03}
      x[    1]={ 2.24531e-02,  3.62402e-03, -8.81686e-03}
      x[    2]={ 1.76530e-02,  5.75658e-03, -6.89898e-03}
      x[    3]={ 1.40843e-02,  1.05042e-02, -5.93055e-03}
      x[    4]={ 7.69775e-03,  1.05042e-02, -4.27620e-03}
      x[    5]={ 5.82995e-03,  1.53628e-02, -2.67087e-03}


Presently, one can generate a trajectory from some given coordinates as:

# iterate over the new frames to write trajectory
for frame,coords in enumerate(newtraj):
        ts._pos[:] = coords     # change coords of current in-memory time step
        ts.frame = frame         # manually change the frame number
        W.write(ts)
W.close() 

But that puts zero velocities and does not include the mode index. That renders 
the trajectory unacceptable to Gromacs as a PCA trr file.

Original issue reported on code.google.com by rcreh...@gmail.com on 21 Sep 2011 at 10:06