[gmx-users] -don (g-hbond)

[Justin A. Lemkul]

atila petrosian wrote:
> Dear Justin
> 
>  
> 
> Header of file is as follow:
> 
>  
> 
>  
> 
> @    title "Donor properties" 
> 
> @    xaxis  label "Time (ps)" 
> 
> @    yaxis  label "Number"    
> 
> @TYPE xy                      
> 
> @ view 0.15, 0.15, 0.75, 0.85 
> 
> @ legend on                   
> 
> @ legend box on               
> 
> @ legend loctype view         
> 
> @ legend 0.78, 0.8            
> 
> @ legend length 2             
> 
> @ s0 legend "Nbound"          
> 
> @ s1 legend "Nfree"   
> 
> 1.950e+04      18     185
> 
> 1.950e+04      17     186
> 
> 1.951e+04      19     184
> 
> 1.951e+04      16     187
> 
> 1.952e+04      18     185
> 
> 1.952e+04      17     186
> 
> 1.952e+04      16     187
> 
> 1.953e+04      18     185
> 
> 1.953e+04      18     185       
> 
>  
> 
> What do Nbound and Nfree denote exactly?

 From a quick look through the code (analyse_donor_props in gmx_hbond.c), it 
would appear that Nbound = number of donors in H-bonds, Nfree = those that are not.

> summation of Nbound and Nfree is constant. what is that (summation)?
>  
> 

The number of donors is constant, and they can only be classified as one of two 
states: involved in an H-bond or not.

-Justin

-- 
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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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