[gmx-users] g_dist issue( Out put file)

[teklebrh at ualberta.ca]

The following is the out put.

# This file was created Mon Aug 23 11:18:45 2010
# by the following command:
# /home/software/gromacs/3.3.3/bin/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
#
# /home/software/gromacs/3.3.3/bin/g_dist is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@    title "Distance"
@    xaxis  label "Time (ps)"
@    yaxis  label "Distance (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000000    0.0000000    0.0000000    0.0000000    0.0000000
19002.0000000    0.0000000    0.0000000    0.0000000    0.0000000
19004.0000000    0.0000000    0.0000000    0.0000000    0.0000000
19006.0000000    0.0000000    0.0000000    0.0000000    0.0000000
19008.0000000    0.0000000    0.0000000    0.0000000    0.0000000
19010.0000000    0.0000000    0.0000000    0.0000000    0.0000000
19012.0000000    0.0000000    0.0000000    0.0000000    0.0000000
19014.0000000    0.0000000    0.0000000    0.0000000    0.0000000
19016.0000000    0.0000000    0.0000000    0.0000000    0.0000000
19018.0000000    0.0000000    0.0000000    0.0000000    0.0000000
19020.0000000    0.0000000    0.0000000    0.0000000    0.0000000
19022.0000000    0.0000000    0.0000000    0.0000000    0.0000000
19024.0000000    0.0000000    0.0000000    0.0000000    0.0000000
19026.0000000    0.0000000    0.0000000    0.0000000    0.0000000
19028.0000000    0.0000000    0.0000000    0.0000000    0.0000000
19030.0000000    0.0000000    0.0000000    0.0000000    0.0000000
19032.0000000    0.0000000    0.00000



Quoting 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
>
>
>
> -- 
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