[gmx-users] Re: hydrogen bonds

[Vasilis Georgilas]

This is from my topology file for palmitic acid.

You say a should make a group of all O, of OM and of HO.

But for the calculation I need the angle between hydrogene - donor -
acceptor.
So my index file should be in triplets, right?? this means I should type a
HO a OA a O.

Correct?

thank you


[ atoms ]
;   nr    type   resnr  residu    atom    cgnr        charge
     1      HO       1    PLM     H2        1     0.370
     2      OM       1    PLM     O4        1    -0.460
     3       C       1    PLM     C3        1     0.42
     4       O       1    PLM     O5        1    -0.45
     5     CP2       1    PLM     C4        2     0.12
     6     CP2       1    PLM     C5        3     0
     7     CP2       1    PLM     C6        4     0
     8     CP2       1    PLM     C7        5     0
     9     CP2       1    PLM     C8        6     0
    10     CP2       1    PLM     C9        7     0
    11     CP2       1    PLM     C10       8     0
    12     CP2       1    PLM     C11       9     0
    13     CP2       1    PLM     C12      10     0
    14     CP2       1    PLM     C13      11     0
    15     CP2       1    PLM     C14      12     0
    16     CP2       1    PLM     C15      13     0
    17     CP2       1    PLM     C16      14     0
    18     CP2       1    PLM     C17      15     0
    19     CP3       1    PLM     C18      16     0
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