[gmx-users] Double counting of h-bonds g_hbond:issue

[Udaya Dahal]

Hi All,

When I used the g_hbond the hydrogen bonding i was getting was quite good
but when I checked the index file i find double counting of the bonds. So
far, it seems to me that g_hbond is giving higher than the real hydrogen
bonds present in the system. For eg. in the following OW-HW-oxygen, we see
there are two bonds between 109(OW) and 110(HW) for two different polymer
oxygens.

Can anyone explain this issue?

     76     77     12
    100    101     47
    109    110     40------->1 (same hydrogen with two different oxygens)
    109    110     54------->2(same hydrogen with two different oxygens)
    211    212     54
    211    212     68
    337    338     68
    343    344      5
    343    344     19
    403    404     61
    487    488      5
    511    512     26
    511    512     40
    538    539     33
    592    593     12
    592    593     26

Hbnum.xvg shows
hydrogen bonds             pairs within 0.35
16                                       8


Regards,
Udaya