[gmx-users] H-bond autocorrelation doubts

[bipin singh]

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> 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>
>
>> 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 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>
>> 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 755erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
>
>


-- 
*
---------------------------------
Thanks and regards
Bipin Singh
*
*
*
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