[gmx-users] Writing initial coordinates to trajectory files

Brian Helfrich brian at nanorex.com
Fri Nov 30 18:55:20 CET 2007

Berk Hess wrote:
> The initial coordinates are written immediately to the trr file,
> although the file system might buffer data, you so could have to wait
> until some more frames have been written.

Thanks, I see that now. It seems that somewhere between grompp and 
mdrun's initial trajectory output, my initial coordinates did change 
ever so slightly:

    1LYSH     N    1   2.105   0.744   2.070
    1LYSH    H1    2   2.056   0.668   2.027
    1LYSH    H2    3   2.190   0.761   2.021

   natoms=      9035  step=         0  time=0.0000000e+00  lambda=         0
      x[    0]={ 2.10518e+00,  7.43687e-01,  2.07004e+00}
      x[    1]={ 2.05600e+00,  6.68002e-01,  2.02700e+00}
      x[    2]={ 2.19043e+00,  7.61087e-01,  2.02075e+00}

But step 0 coordinates are output as you said, thanks.

Brian Helfrich

More information about the gromacs.org_gmx-users mailing list