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

teklebrh at ualberta.ca teklebrh at ualberta.ca
Mon Aug 23 20:24:11 CEST 2010


Dear Justine,

I got it and works fine.

@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000000    0.7047197   -0.3054392   -0.1559912    0.6156325
19002.0000000    0.7591453   -0.2601027   -0.2659363    0.6617599
19004.0000000    0.7763510   -0.3043177   -0.2214912    0.6790090
19006.0000000    0.7837191   -0.2325068   -0.2653693    0.6998110
=============================

I have another question for you. Does g_analyse is oky to use to get  
the mean separation.

g_anayze -f XXXX.xvg -av average.xvg -errbar enum -b 19000 -e 20000

is the column 1 and two is correct means time and distance respectively.

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


Is the same process apply for the g-rdf?

  Group     0 (      System) has 28708 elements
>> Group     1 (         PAP) has   512 elements
>> Group     2 (         HEP) has 28196 elements
>> Group     3 (        RING) has    20 elements

I want to calculate g(r) for PAP molecules...... but by default it is  
there does I need to create two PAP_1 and PAP_2 to get the g(r). To  
get for the

PAP-PAP g(r) value. Or just need to select 1 twice?

Rob


Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> 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
>>>>>
>>>>>
>>>>>
>>>>> -- 
>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at http://www.gromacs.org/search  
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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
>>>
>>> ========================================
>>> -- 
>>> gmx-users mailing list    gmx-users at gromacs.org
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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
>
> ========================================
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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