<font style="color:rgb(0, 0, 0)" size="2">Emanuel,<div class="im"><br><br>Am trying out the procedure u have mentioned but on the other hand i found out a article which mentions does the same.<br><br><a href="https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html" target="_blank">https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html</a><br>
<br>The article states- <br><br></div>use the g_hbond
</font><font style="color:rgb(0, 0, 0)" size="2"> program to analyse hydrogen
bonds. First select protein twice, to get the intramolecular hydrogen
bonds, then select protein and water to get the protein-water h-bonds. Compare the numbers,
and their fluctuations. Is there a trend in the graphs, or a
correlation between them? You
can also compute the residence time of the water molecules on the
different functional groups of the protein., e.g. the Ala sidechain.
For this we will have to make an index file first:<div class="im"><br>
% make_ndx -f after_em_sol << EOF<br>
a OW<br>
q<br>
EOF<br>
% g_hbond -contact -n index -ac -r 0.6
-b 200<br></div>
In the g_hbond command select Sidechain and OW. The -c option computes
the autocorrelation function of the contact time between Cβ and OW.
View the file hbac.xvg using xmgrace. Use xmgrace to integrate the ACF,
this will give you the correlation time. Is it higher or
lower than you expected? Why?<div class="im"><br>
Now do the same analysis for interactions between Carbonyl groups and
Amide groups and water oxygens. For these analyses you should put the
distance to 0.35, the largest hydrogen bonding distance. Compare the
residence times with that on the hydrophobic sidechain.<br><br><br>as
it mentioned the -contact wouldnt include any H bonds between the
groups. but i didnt understand what does OW states cause already there
is an option for water.<br>
does this procedure be good for an residence time.<br><br>-Aiswarya</div></font>
<br><br><div class="gmail_quote">On Thu, Aug 25, 2011 at 5:18 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 25/08/2011 12:00 AM, <a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a> wrote:
<blockquote type="cite">
<pre>Mark,
The residence time equation goes like this-
P(r)= function (N(t) - N(t+r))dt
Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t.</pre>
</blockquote>
<br></div>
So that's the autocorrelation of the existence function. Now you
need a geometric criterion for existence. Note that g_hbond with
well-constructed groups will calculate the autocorrelation of the
existence function for an H-bond. See g_hbond -h.<br>
<br>
g_dist, some scripting and g_analyse might be necessary for other
criteria.<br><font color="#888888">
<br>
Mark</font><div class="im"><br>
<br>
<blockquote type="cite">
<pre>Aiswarya
------Original Message------
From: Mark Abraham
To: Aiswarya Pawar
Subject: Re: [gmx-users] Hydrogen existence time
Sent: 24 Aug 2011 6:09 PM
On 24/08/2011 10:31 PM, <a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a> wrote:
</pre>
<blockquote type="cite">
<pre>Any idea how can I calculate the residence time of water.
</pre>
</blockquote>
<pre>First, seek define what you mean to calculate. If you can't write an
equation down for it, you can't calculate it.
Mark
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!</pre>
<br>
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<br>
</blockquote>
<br>
</div></div>
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