[gmx-users] g_hbond distance distribution problem

[Xavier Periole]

> 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.
> 
>> 
>>    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.
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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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