[gmx-users] H-bond autocorrelation doubts

[Erik Marklund]

It computes the same acf, but the thermodynamic/kinetic calculations 
give different results for different -temp, don't they?

Erik

bipin singh skrev 2011-02-28 18.01:
> Thanks for your suggestions.....
> Can you please give some explanation for my second doubt...
>
> 2011/2/28 André Farias de Moura <moura at ufscar.br <mailto:moura at ufscar.br>>
>
>     the manual does not enclose all the necessary knowledge for any
>     kind of MD
>     simulation or analyses, so you have to read some papers and
>     textbooks as
>     well.as <http://well.as> I've already pointed out, g_hbond reads
>     the whole set of frames, but the
>
>     results are meaningful (in the sense of having a homogeneous
>     variance) only
>     up to half of the size of the sample. if you need the correlation
>     function for a
>     longer time lag, increase the length of your simulation. that way,
>     your ACF
>     should remain meaningful.
>
>     best
>
>     Andre
>
>     On Mon, Feb 28, 2011 at 10:36 AM, bipin singh
>     <bipinelmat at gmail.com <mailto:bipinelmat at gmail.com>> wrote:
>     >
>     > Hello,
>     >
>     > I am usng g_hbond to calculate H bond auto correlation during
>     the simulation
>     > for two residues in my system, I have two doubts regarding this:
>     >
>     > 1)How to use -acflen to calculate autocorrelation for all the
>     frames instead
>     > of half of the frames
>     > 2) What is the use of -temp option in calculating the
>     autocorrelation
>     > because it is giving same result whether you use 298K or 500K
>     >
>     > I have read the manual but I am not clear about these functions.
>     > --
>     > ---------------------------------
>     > Thanks and regards
>     > Bipin Singh
>     >
>     >
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> -- 
> /
> ---------------------------------
> Thanks and regards
> /Bipin Singh/
> /
> /
> /
>


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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