[gmx-users] Problem with gmx-distance

Timofey Tyugashev tyugashev at niboch.nsc.ru
Wed Sep 16 15:45:50 CEST 2015

I want to get the distance between atoms 3770 and 5182 in my trajectory
After consulting with the Manual I write command:
gmx distance -n ind2.ndx -f trj1_WT_md_40.xtc -s wt_md.gro -oav 
distav.xvg -oall dist.xvg
and index file ind2.ndx:
[ LYS_241_ODG_C1' ]
3770 5182

The program responds like this:

Available static index groups:
  Group  0 "LYS_241_ODG_C1'" (2 atoms)
Specify any number of selections for option 'select'
(Position pairs to calculate distances for):

If I pick 0, it responds 'Selection '0' parsed' and then nothing happens.
What to do next? The manual is incredibly murky and there are no 
examples in the net.

More information about the gromacs.org_gmx-users mailing list