[gmx-users] g_hbond and Autocorrelation function

[David van der Spoel]

On 2/22/10 9:47 AM, leilakarami at aol.com wrote:
>
> Hi
> I used g_hbond for analyzing hydrogen bonds.
> What is difference between [s0 legend "Ac\sfin sys\v{}\z{}(t)"] and [s1
> legend "Ac(t)"] in hbac.xvg file in below?

First one is "corrected" for the fact that in a finite system the ACF 
does not go to zero, since HBs will reform after a long time. There is a 
better way to do this, by following the PBC of each molecule (as in mean 
square deviation). This will be implemented in the next version.


> @ title "Hydrogen Bond Autocorrelation"
> @ xaxis label "Time (ps)"
> @ yaxis label "C(t)"
> @ s0 legend "Ac\sfin sys\v{}\z{}(t)"
> @ s1 legend "Ac(t)"
> @ s2 legend "Cc\scontact,hb\v{}\z{}(t)"
> @ s3 legend "-dAc\sfs\v{}\z{}/dt"
> 0 1 1 -0.00217462 0.275102
> 2 0.4543 0.847763 0.0871663 0.144609
> 4 0.421563 0.83863 0.0883458 0.0141166
> 6 0.397833 0.83201 0.0893797 0.0101501
> 8 0.380963 0.827303 0.0896131 0.00766257
> 10 0.367183 0.823459 0.0899727 0.00601236
> 12 0.356914 0.820594 0.0902401 0.00526451
> 14 0.346125 0.817584 0.0900176 0.004734
> Are both of them Are both of them Autocorrelation function?
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se