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It computes the same acf, but the thermodynamic/kinetic calculations
give different results for different -temp, don't they?<br>
<br>
Erik<br>
<br>
bipin singh skrev 2011-02-28 18.01:
<blockquote
cite="mid:AANLkTingv-qyDT8mYy6U+oDzzbDW9Okz6_ka2RuiZorz@mail.gmail.com"
type="cite">Thanks for your suggestions.....<br>
Can you please give some explanation for my second doubt...<br>
<br>
<div class="gmail_quote">2011/2/28 André Farias de Moura <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:moura@ufscar.br">moura@ufscar.br</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">the manual does not enclose all the
necessary knowledge for any kind of MD<br>
simulation or analyses, so you have to read some papers and
textbooks as<br>
<a moz-do-not-send="true" href="http://well.as">well.as</a>
I've already pointed out, g_hbond reads the whole set of
frames, but the<br>
</blockquote>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
results are meaningful (in the sense of having a homogeneous
variance) only<br>
up to half of the size of the sample. if you need the
correlation<br>
function for a<br>
longer time lag, increase the length of your simulation. that
way, your ACF<br>
should remain meaningful.<br>
<br>
best<br>
<br>
Andre<br>
<div>
<div class="h5"><br>
On Mon, Feb 28, 2011 at 10:36 AM, bipin singh <<a
moz-do-not-send="true"
href="mailto:bipinelmat@gmail.com">bipinelmat@gmail.com</a>>
wrote:<br>
><br>
> Hello,<br>
><br>
> I am usng g_hbond to calculate H bond auto
correlation during the simulation<br>
> for two residues in my system, I have two doubts
regarding this:<br>
><br>
> 1)How to use -acflen to calculate autocorrelation for
all the frames instead<br>
> of half of the frames<br>
> 2) What is the use of -temp option in calculating the
autocorrelation<br>
> because it is giving same result whether you use 298K
or 500K<br>
><br>
> I have read the manual but I am not clear about these
functions.<br>
> --<br>
> ---------------------------------<br>
> Thanks and regards<br>
> Bipin Singh<br>
><br>
><br>
</div>
</div>
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<br>
<br clear="all">
<br>
-- <br>
<font color="#3333ff"><i><font face="arial, helvetica, sans-serif">
<div>---------------------------------<br>
Thanks and regards<br>
</div>
<div><span style="font-family: arial; font-style: normal;"><i><font
face="arial, helvetica, sans-serif">Bipin Singh</font></i></span></div>
</font></i></font>
<div><font color="#3333ff" face="arial, helvetica, sans-serif"><i><br>
</i></font></div>
<br>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
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