[gmx-users] g_dist issue( Out put file)
teklebrh at ualberta.ca
teklebrh at ualberta.ca
Mon Aug 23 19:54:44 CEST 2010
Dear Justine,
Reading file PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr, VERSION 3.3.3
(single precision)
Group 0 ( System) has 28708 elements
Group 1 ( PAP) has 512 elements
Group 2 ( HEP) has 28196 elements
Group 3 ( RING) has 20 elements
Select a group: 3
Selected 3: 'RING'
Select a group: 3
Selected 3: 'RING'
Reading frame 0 time 19000.000
Back Off! I just backed up DistPAP8HEP.xvg to ./#DistPAP8HEP.xvg.8#
Last frame 500 time 20000.000
====================
which means I have to create two index file for two rings Ring_1 AND
Ring_2 and choose both of them. If I am correct.
Rob
Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>
> 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
>
> ========================================
> --
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