[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.


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