>------------------------------
>
>Message: 4
>Date: Sun, 18 May 2008 00:50:30 +0200
>From: "Xavier Periole" <[EMAIL PROTECTED]>
>Subject: Re: [gmx-users] g_hbond distance distribution problem
>To: Discussion list for GROMACS users <[email protected]>
>Message-ID: <[EMAIL PROTECTED]>
>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: [EMAIL PROTECTED]
>>> =========================================
>>>
>>>
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