[gmx-users] H-bond autocorrelation doubts

[Erik Marklund]

That's odd, unless the values are -666. I just looked at the source 
code, and it seems as if the temperature is passed on to the right 
functions.

Erik

bipin singh skrev 2011-02-28 19.34:
> NO, its giving same result no matter what temperature you provide 
> using -temp option.
>
> On Mon, Feb 28, 2011 at 23:55, Erik Marklund <erikm at xray.bmc.uu.se 
> <mailto:erikm at xray.bmc.uu.se>> wrote:
>
>     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  <mailto:erikm at xray.bmc.uu.se>     http://folding.bmc.uu.se/
>
>
>
>
> -- 
> /
> ---------------------------------
> 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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