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

[Justin A. Lemkul]

teklebrh at ualberta.ca wrote:
> 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
> 

You say you want the distance between two rings, but you only showed an index 
group for one of them (presumably), and the fact that you've gotten all zeroes 
as a result would suggest that you chose the same group twice for the distance 
calculation.  Which groups did you select?  Do they correspond to two, 
non-overlapping index groups?

-Justin

> 
> 
> 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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>>
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================