Dear Mark and David,
Thanks you, i will check the paper very carefully and try again.
regards,
Rama
On Sat, Feb 27, 2010 at 1:13 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> 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
>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>> sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
>>
>> http://folding.bmc.uu.se
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>>
>> --
>> Postdoctoral Research Scholar,
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>>
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Department of Chemistry,
University of Nevada, Reno.
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