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

[David van der Spoel]

On 2010-02-27 09.31, 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?

The correlation time is a result from the calculation. There are many 
definitions possible. One is the integral of C(t). JPCB 110 (2006) p. 
4393 gives explanations for hbonds.
>
> best
> Rama
>
> 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>
>     http://folding.bmc.uu.se
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> --
> Postdoctoral Research Scholar,
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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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se