[gmx-users] H-bond autocorrelation doubts

André Farias de Moura moura at ufscar.br
Mon Feb 28 17:37:52 CET 2011

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

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.



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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