[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
>>>
>>> ========================================
>>> --
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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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