[gmx-users] Re: g_hbond modification
Robin C. Underwood
rcunderw at purdue.edu
Mon Nov 8 22:10:15 CET 2010
Thanks for the prompt reply Justin, but I'm still not convinced that I can
extract the information I seek from the g_hbond program without modification.
I realize this wasn't clear in my initial message: I would like to know how many
OH donors are not participating in ANY hydrogen bonds.
If I calculate the number of non-hydrogen bound OH donors as the difference
between the number of pairs that meet the distance requirement, and the actual
number of hydrogen bonds (column 3 minus column 2 in hbnum), then I would be
over-counting, as this does not exclude pairs with OH donors that are also
included in a hydrogen bond with another O acceptor.
Quoting "Robin C. Underwood" <rcunderw at purdue.edu>:
> I would like to modify the g_hbond code (or preferably, know how to
> g_hbond if it is already capable) to count the number of non-hydrogen bound
> water OH donors in a simulation. I define a non-hydrogen bound donor as one
> does not meet the distance requirement, or one that may meet the distance
> requirement for a hydrogen bond, but does not meet the angle requirement.
> An inferred value of non-hydrogen bound OH donors is not exact because there
> not a rigorously defined maximum value for the number of hydrogen bonds per
> water, (e.g. a single OH donor may qualify as part of a hydrogen bond at two
> adjacent water's O-acceptor sites, making the maximum possible number of
> hydrogen bonds for the water of this particular OH donor greater than 4).
> Is there a way to implement g_hbond to do this? If not, any specific
> on what to consider, and how to modify the g_hbond source code to count
> non-hydrogen bound water OH donors is greatly appreciated.
> Robin C. Underwood
> Chemistry Department
> 560 Oval Drive
> West Lafayette, IN 47907
Robin C. Underwood
560 Oval Drive
West Lafayette, IN 47907
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