[gmx-users] Measuring Atom Distances

[Javad Azadi]

Hi!

I am trying to measure the distance with releation to steps between two
unconnected atoms for any trajectory.  I am able to do this in VMD by labeling
the atoms and saving the file.  It takes forever, but the format is exactly
how I need it: column one is step number and column two is distance.  I
thought I could do it using g_bond, but after defining the two atoms using
make_ndx and trying to run >g_bond_d -f traj.xtc -n index.ndx -s traj.tpr -o
dist
I get an error saying "Fatal error: No distribution... (i0 = 999, i1 = 1)? ? !
! ? !".  I do not want a distribution, but a plot of step vs distance between
atom a and b.

Thank you,
Javad Azadi
Undergraduate Researcher
The Ohio State University
jazadi at chemistry.osu.edu