[gmx-users] g_dist issue( Out put file)
Justin A. Lemkul
jalemkul at vt.edu
Mon Aug 23 20:00:02 CEST 2010
teklebrh at ualberta.ca wrote:
> 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.
>
Yes. Otherwise the distance from the center of mass of RING is calculated
relative to the center of mass of RING, which by definition will always be zero.
-Justin
> 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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>>
>
>
--
========================================
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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