[gmx-users] g_hbond modification

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 8 19:27:21 CET 2010

Robin C. Underwood wrote:
> 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.  

I think this is already present in the output.  The third column of the output 
hbnum.xvg is "Pairs within 0.35 nm," which are pairs that meet the distance 
requirement, but not the angle requirement.  For a properly-constructed index 
group, this sounds like it may give you what you want.


> 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 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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