[gmx-users] % of existence of hydrogen bond

Ran Friedman r.friedman at bioc.uzh.ch
Thu Oct 29 15:37:29 CET 2009

You can use g_hbond -num and write a small script to calculate the
percentage of h-bond existence per frame by calculating the number of
frames for which a h-bond exists.
Good luck,

Moutusi Manna wrote:
> Dear all,
>         I am dealing with a POPC+PEPTDE+WATER system. Basic residues
> of the peptide make hydrogen bonds with lipid headgroup (as reflected
> from g_rdf analysis) and the number of hydrogen bonds formed can be
> calculated from g_hbond program. Now, i want to calculate the % of
> trajectory time for which a bond between a particular group (say LYS
> and lipid headgroup po4) exist. -hbm gives a .xpm matrix, on solving
> (using xpm2ps) that i got a .eps file, which is a picture file of
> h_bond existence map, but the data sheet is not given.
> Can any one help me to solve this problem?
> With regards,
> Moutusi Manna
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