[gmx-users] g_hbond modification

Robin C. Underwood rcunderw at purdue.edu
Mon Nov 8 19:09:12 CET 2010

I would like to modify the g_hbond code (or preferably, know how to implement
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 that
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 is
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 information
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

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