[gmx-users] Output of g_hbond

[Hu Qiu]

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.

 

I don't what's wrong.

 

Thanks 

 

Hu Qiu

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