[gmx-users] H-bond autocorrelation doubts

[bipin singh]

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
*
*
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