[gmx-users] g_hbond distance distribution problem

[David van der Spoel]

Dechang Li wrote:
> Dear all,
> 
>      I used command g_hbond to calculated the distance distribution of hbonds
> in my system. There are two columns in the file hbdist.xvg, as showed follow:
> 
> @    title "Hydrogen Bond Distribution"
> @    xaxis  label "Hydrogen - Acceptor Distance (nm)"
> @    yaxis  label ""
> 
> @TYPE xy
>     0.0025          0
>     0.0075          0
>     0.0125          0
>     0.0175          0
>     0.0225          0
>     0.0275          0
>     0.0325          0
>     0.0375          0
>     0.0425          0
>     0.0475          0
>     ......          ...
> 
>    I think the second column is the distance distribution of hbonds, so the 
> summation of the second column should be 1, right? However, the summation 
> in my file is 200, what is the problem?

Could be, then it is ot normalized.  You can do that easily in xmgrace.

> 
>    And the first column refered to "Hydrogen - Acceptor Distance (nm)" , should
> it be the distance of donors and acceptor? Am I right?

At what position is the top of the distribution?
If it is at 0.17 nm it is HA as it says.
> 
>  
> 
> 
> 
> Best regards,
> 2008-5-17
> 
> 
> ========================================= 
> Dechang Li, PhD Candidate
> Department of Engineering Mechanics
> Tsinghua University
> Beijing 100084
> PR China 
> 
> Tel:   +86-10-62773779(O) 
> Email: lidc02 at mails.tsinghua.edu.cn
> =========================================
> 
>   
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se