[gmx-users] g_dist issue

[teklebrh at ualberta.ca]

Dear Gromacs users,

I run my simulation for 20ns and want to extract aromatic-aromatic  
distance to see the stacking issue. But I am unable to get the value.

I have 24 molecules in my simulation and filled with solvents.

My index file is like that:

[ System ]
    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
   46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
   61   62
   '''''''
   '''''''
   '''''''
   ''''''

[ RING ]
   19   20   21   22   23   24   25   26   27   28   29   30
   32   34   37   38   39   40   42   44

This is the ring I created plane in the index file.

I used this command line

g_dist -f PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 20000 -o  
DistPAP8HEP.xvg

but got the following like

I want to get the mean separation distance between two consecutive  
polyaromatic rings along the axis of stacking

can someone help.

rob