[gmx-users] g_hbond distance distribution problem

[David van der Spoel]

Dechang Li wrote:
>> ------------------------------
>>
>> Message: 4
>> Date: Sun, 18 May 2008 00:50:30 +0200
>> From: "Xavier Periole" <X.Periole at rug.nl>
>> Subject: Re: [gmx-users] g_hbond distance distribution problem
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <web-76326296 at mail3.rug.nl>
>> Content-Type: text/plain;charset=utf-8;format="flowed"
>>
>>> 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?
> 
>> The sum itself should not be one but the integral of the curve should be
>> one. Considering the bin you have the 200 makes sense. Try to integrate.
>>> Could be, then it is ot normalized.  You can do that easily in xmgrace.
> 
>     I integrated it, the result is 1.0 exactly.
> 
>>>>    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.
>        
>     The top of the distribution is about 0.3 nm, so it is the D-A distance? 
Yes. Will fix it.

> 
> 
> 
>>>>  
>>>>
>>>>
>>>>
>>>> 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