[gmx-users] g_dist issue( Out put file)
Justin A. Lemkul
jalemkul at vt.edu
Mon Aug 23 20:33:20 CEST 2010
teklebrh at ualberta.ca wrote:
> 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.
>
I don't see why not. That's pretty much the main function of g_analyze.
> 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.
>
Per the notation in the .xvg file, yes.
> =========================
>
>
> 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?
Try it and see :)
-Justin
>
> 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 before
>>>>>> posting!
>>>>>> Please don't post (un)subscribe requests to the list. Use thewww
>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>>
>>>>>>
>>>>>
>>>>
>>>> --
>>>> ========================================
>>>>
>>>> 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
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before
>>>> posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>
>>>>
>>>
>>>
>>
>> --
>> ========================================
>>
>> 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
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list