[gmx-users] correlation function 'time value' ?

Mark Abraham Mark.Abraham at anu.edu.au
Sat Feb 27 10:13:55 CET 2010

```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
> <spoel at xray.bmc.uu.se <mailto:spoel at 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
>
>
>     --
>     David van der Spoel, Ph.D., Professor of Biology
>     Dept. of Cell & Molec. Biol., Uppsala University.
>     Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
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>

```