GROMACS

gmx distance -oxyz (v5.1.2) has data like the text posted below. The comments could be more useful if they indicated that the data was <time> <x1> <y1> <z1> ... <xN> <yN> <zN>

Posting this based on the gmx users thread here:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-February/110917.html

# This file was created Tue Feb  7 21:36:27 2017
# Created by:
#                 :-) GROMACS - gmx distance, VERSION 5.1.2 (-:
#
# Executable:   /Users/exe/GROMACS/exec/gromacs-5.1.2/serial/bin/gmx
# Data prefix:  /Users/exe/GROMACS/exec/gromacs-5.1.2/serial
# Command line:
#   gmx distance -f FEMS.gro -s FEMS.tpr -oxyz out.xvg
# gmx distance is part of G R O M A C S:
#
# Good gRace! Old Maple Actually Chews Slate
#
@    title "Distance" 
@    xaxis  label "Time (ps)" 
@    yaxis  label "Distance (nm)" 
@TYPE xy
      0.000    0.089   -0.036    0.016    0.112    0.029   -0.057   -0.088    0.130   -0.077   -0.109   -0.055    0.054    0.120   -0.058    0.024   -0.265    0.147   -0.064   -0.108    0.013    0.010   -0.046    0.126   -0.060   -0.192   -0.072   -0.060    0.129    0.061   -0.153   -0.060    0.149    0.206    0.166    0.119   -0.043   -0.011   -0.089    0.310    0.115   -0.172    0.034    0.020    0.014    0.108    0.047   -0.206    0.005   -0.003   -0.147   -0.014    0.085   -0.044    0.228   -0.097   -0.093   -0.074   -0.098    0.185   -0.129