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.
-Justin
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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