[gmx-users] g_hbond distance distribution problem

[Dechang Li]

>------------------------------
>
>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? 



>>> 
>>>  
>>> 
>>> 
>>> 
>>> 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
>>> =========================================
>>> 
>>>