On 27/02/2010 7:31 PM, Ramachandran G wrote:
Dear Dr. van der Spoel:
Thanks for the clarification in your reply. One more thing I was just
curious is that, for C(t) = < f(x).f(x+t) >,
what is the default value for t, which is often called "correlation
time", in gromacs for correlation function calculation, especially in
"g_hbond",
and/or is it possible to customize the t in gromacs?
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
Wolff, U. Comput. Phys. Commun. 2004, 156, 143-153.
Madras, N.; Sokal, A. D. J. Stat. Phys. 1988, 50, 109-186.
useful.
Mark
On Fri, Feb 26, 2010 at 10:03 PM, David van der Spoel
<sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>> wrote:
On 2010-02-27 03.27, Ramachandran G wrote:
Hi gromacs users:
As you know autocorrelation function C(t)
C(t) = <f(0).f(t)>
't' value can start from 0 but, i would like to know what value does
gromacs use, more specifically for g_hbond.
Can anyone help me? Thank you.
Rama
The <> tell you that all time origins x are used, so
C(t) = < f(x).f(x+t) >_x
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
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