[gmx-users] g_analyze doubt

[aiswarya pawar]

Hi,

I have used the command =

g_dist -f md.xtc -s md.tpr -n index.ndx

which gives an output of data=

  0.0000000    0.6259024    0.3880000    0.3610001   -0.3329997
   1.0000000    0.6778775    0.2590003    0.5939999   -0.1989999
   2.0000000    0.6759030    0.2529998    0.5939999   -0.2000003
   3.0000000    0.6463353    0.1690001    0.5680003   -0.2579999
   4.0000000    0.6808891    0.2639999    0.6050000   -0.1669998
   5.0000000    0.6883561    0.3090000    0.5920000   -0.1670003
   6.0000000    0.6201660    0.2769997    0.5139999   -0.2090001
   7.0000000    0.6832005    0.2910001    0.5809999   -0.2110000
   8.0000000    0.6472999    0.2960002    0.5339999   -0.2150002
   9.0000000    0.6542692    0.1880000    0.5400000   -0.3180003
  10.0000000    0.6725602    0.3230002    0.5780001   -0.1180000
  11.0000000    0.6138712    0.3470001    0.4769998   -0.1700001
  12.0000000    0.6999645    0.2860000    0.6150002   -0.1729999
  13.0000000    0.6504593    0.1200001    0.6160002   -0.1710000
  14.0000000    0.6447160    0.2110000    0.5869999   -0.1629996
  15.0000000    0.6645610    0.2040000    0.5710001   -0.2720003
  16.0000000    0.6481276    0.2330003    0.5560002   -0.2379999
  17.0000000    0.6511113    0.2240002    0.5609999   -0.2430000
  18.0000000    0.7119258    0.2650001    0.6220002   -0.2230000
  19.0000000    0.6653563    0.0929999    0.6170001   -0.2309999
  20.0000000    0.6881638    0.2520001    0.6070004   -0.2040000
  21.0000000    0.7161944    0.2090001    0.6220002   -0.2870002
  22.0000000    0.6587778    0.1400001    0.6020002   -0.2279997
  23.0000000    0.5798631    0.0170002    0.5160003   -0.2639999
  24.0000000    0.5862564    0.0390000    0.5239997   -0.2599998
  25.0000000    0.6923014   -0.1240001    0.5520000   -0.3990002
  26.0000000    0.5787479   -0.0899997    0.5050001   -0.2680001
  27.0000000    0.5776323   -0.2589998    0.4730000   -0.2070003
  28.0000000    0.5910018   -0.1630001    0.5250001   -0.2170000
  29.0000000    0.4448786   -0.1570001    0.4020000   -0.1079998
  30.0000000    0.4806164   -0.2160001    0.4000001   -0.1560001
  31.0000000    0.5405830   -0.1700001    0.4730000   -0.1989999
  32.0000000    0.5614526   -0.1080003    0.4930000   -0.2459998
  33.0000000    0.4994450   -0.0730000    0.4500003   -0.2040000
  34.0000000    0.5323368   -0.1420002    0.4830003   -0.1730003


>From this the first column is the time and the second is the water protein
atom distance. so when am using the g_analyze i would use the 1st and 2nd
column for the input? More over now this distances are below 0.8 nm . what
would i do if my data in between shows distance more than 0.8nm.

Thanks
On Wed, Feb 1, 2012 at 6:48 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> aiswarya pawar wrote:
>
>> Dear Gromacs Users,
>>
>> i have data for the distance between the protein and water atoms within a
>> cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze
>> on this data. The time frame in the output data is not continuous because
>> of the cut off provided. So i would like to know how would the g_analyze
>> would compute the data.
>>
>>
>>
> I'm not clear on what you're trying to do.  g_analyze performs simple
> statistical operations (averages, error estimates) on the input data.  If
> there are discontinuities (which I do not understand the nature of), they
> come from the g_dist data, not what g_analyze is doing.
>
> Please provide a more clear description of what you are doing, including
> all relevant commands, and examples of the data files, if necessary.
>
> -Justin
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
Aiswarya  B Pawar

Project Assistant,
Bioinformatics Dept,
Indian Institute of Science
Bangalore
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