[gmx-users] Measuring Atom Distances
jazadi at chemistry.ohio-state.edu
Mon Jul 3 23:59:57 CEST 2006
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
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.
The Ohio State University
jazadi at chemistry.osu.edu
More information about the gromacs.org_gmx-users