Dear Mark and David,<br> Thanks you, i will check the paper very carefully and try again. <br><br>regards,<br>Rama<br><br><div class="gmail_quote">On Sat, Feb 27, 2010 at 1:13 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">On 27/02/2010 7:31 PM, Ramachandran G wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Dr. van der Spoel:<br>
<br>
Thanks for the clarification in your reply. One more thing I was just<br>
curious is that, for C(t) = < f(x).f(x+t) >,<br>
what is the default value for t, which is often called "correlation<br>
time", in gromacs for correlation function calculation, especially in<br>
"g_hbond",<br>
and/or is it possible to customize the t in gromacs?<br>
</blockquote>
<br></div>
t is not the correlation time. t is an arbitrary amount of time, at which the magnitude of C(t) indicates the extent to which f is correlated with itself when a set of samples are examined at time interval t. The (integrated) correlation time is the integral of (normalized) C(t) over 0 < t < infinity. See section 8.5 of the manual. I also found the explanations in<br>
<br>
Wolff, U. Comput. Phys. Commun. 2004, 156, 143-153.<br>
Madras, N.; Sokal, A. D. J. Stat. Phys. 1988, 50, 109-186.<br>
<br>
useful.<br>
<br>
Mark<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
On Fri, Feb 26, 2010 at 10:03 PM, David van der Spoel<br></div><div class="im">
<<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>> wrote:<br>
<br>
On 2010-02-27 03.27, Ramachandran G wrote:<br>
<br>
Hi gromacs users:<br>
As you know autocorrelation function C(t)<br>
<br>
C(t) = <f(0).f(t)><br>
<br>
't' value can start from 0 but, i would like to know what value does<br>
gromacs use, more specifically for g_hbond.<br>
Can anyone help me? Thank you.<br>
<br>
Rama<br>
<br>
The <> tell you that all time origins x are used, so<br>
C(t) = < f(x).f(x+t) >_x<br>
<br>
<br>
--<br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
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