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<div class="gmail_quote">On Tue, Sep 6, 2011 at 2:50 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
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<div class="h5">On 6/09/2011 11:37 PM, Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear Gromacs Users,<br>I am calculating hbonds between my 10 ligands and each residue... How does Gromacs calculate average number of hbonds per timeframe?<br>
Example:<br>for Glycine:<br>Av. num of hbonds/timeframe<br>0.96<br>To check whether that is correct I added all hbonds formed with Glycine during my simulation time over 2000 (each 50ps) timeframes and I obtained value: 2900. If you divide it by 2000 you will never get 0.96 obviously. How does Gromacs calculate it?<br>
</blockquote><br></div></div>Presumably by adding up the number in each time frame and dividing by the number. Unless you have a highly-exposed glycine, forming more than one H-bond seems unlikely, and your 2900 number suggests it's happening lots of times. I expect you're comparing a sum of oranges with a sum of apples, but without more information about what you're doing in your attempt to check, we can't help much. Please be sure to read g_hbond -h, and the legends of any .xvg files you're looking at.<br>
<font color="#888888"><br>Mark</font>
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<div class="h5">Thank you Justin and Mark,<br></div></div></blockquote>
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<div>Yes, just found the mistake... I added pairs within 3.5 A instead of hbonds so the Gromacs calculation is correct. So the value is 0.96 for Glycine. So in this case it is a strong interaction. Are there any criteria to assess strenght of interactions or binding affinity for residues? Was it described anywhere for each residue to specify these values with respect to possible hbonds for each residue (e.g. Glycine - 3)?</div>
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<div>Steven</div>
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