[gmx-users] g_analyze doubt

[Justin A. Lemkul]

aiswarya pawar wrote:
> 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 

Pass this file directly to g_analyze - there's no need for manipulation.  You'll 
get averages of all four distance columns, but of course just take what you need.

> 0.8 nm . what would i do if my data in between shows distance more than 
> 0.8nm.
> 

You said you had g_dist measure distances between protein atoms and the COM of 
water molecules within 0.8 nm, so I don't see how a distance greater than 0.8 nm 
is even possible in this case.

-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

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