[gmx-users] Measuring Atom Distances

David Mobley dmobley at gmail.com
Tue Jul 4 02:25:04 CEST 2006


I think you want g_dist.


On 7/3/06, Javad Azadi <jazadi at chemistry.ohio-state.edu> wrote:
> 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
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