[gmx-users] Output of g_hbond

[Gianluca Santoni]

On 11/23/11 4:12 PM, Hu Qiu wrote:
>
> Hi all,
>
> I am trying to caluculate number of hydrogen bond in my system using 
> the following command:
>
> g_hbond -f model_frame2000.pdb -s md.tpr  -n index_water.ndx -num 
> hbnum.xvg
>
> Where the file model_frame2000.pdb is the coordinate from a frame 
> during my MD simulation, and the index file (index_water.ndx)contains 
> the index six adjacent tip5p water molecules, see following:
>
> 2559 2560 2561 2562 2563 3029 3030 3031 3032 3033 3504 3505 3506 3507 
> 3508
>
> 5354 5355 5356 5357 5358 5394 5395 5396 5397 5398 6049 6050 6051 6052 
> 6053
>
> The arrangement of water oxygen is like this (rectangle), which " - " 
> indicates the distance is less than 0.35 nm.
>
> OW - OW - OW
>
>  |    |    |
>
> OW - OW - OW
>
> The output hbnum.xvg gives
>
> @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 "Hydrogen bonds"
>
> @ s1 legend "Pairs within 0.35 nm"
>
>         -1           4          10
>
> As I know, the 2nd column is the number of Hydrogen bonds, and the 
> 3ird column indicates "the Pairs within 0.35 nm, but with angle > 30". 
> After viewing the stucture in VMD, I found that the number of Hydrogen 
> bond seems to be correct. However,  only 7 pairs of water oxygen 
> within 0.35 nm can be found (see above for the schematic drawing of 
> water arrangement), thus "the Pairs within 0.35 nm, but with angle > 
> 30"should be 7-4 = 3, which is significantly lower than the value (10) 
> obtained in hbnum.xvg.
>
Third column should be simply pairs within 0.35nm, at any angle.

> I don't what's wrong.
>
> Thanks
>
> Hu Qiu
>
>
>


-- 
Gianluca Santoni,
Institut de Biologie Structurale
41 rue Horowitz
Grenoble
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