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: [EMAIL PROTECTED]
=========================================
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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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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