[gmx-users] meaning of results of g_hbond -ac

[Erik Marklund]

* Time
* Ac(hbond) with correction for the fact that a finite system is being simulated.
* Ac(hbond) without correction
* Cross correlation between hbonds and contacts (see the papers by Luzar&Chandler and van der Spoel that are mentioned in the stdout from g_hbond)
* Derivative of second column.

On 18 Jul 2013, at 04:51, Wu Chaofu <xiaowu759 at gmail.com> wrote:

> Dear gmxers,
> By running the command g_hbond -ac, a resulting .xvg file is generated,
> which is attached below. In that file, there are five columns. I guess
> that, the first column is time, the second the HB autocorrelation function.
> But what are the other columns denoted by s1, s2, s3? Thanks a lot for any
> reply.
> Yours sincerely,
> Chaofu Wu
> 
> # This file was created Wed Jul 17 09:49:34 2013
> # by the following command:
> # g_hbond -f iconf.xtc -s conf.tpr -n -ac ihbac2.xvg
> #
> # g_hbond is part of G R O M A C S:
> #
> # GROtesk MACabre and Sinister
> #
> @    title "Hydrogen Bond Autocorrelation"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "C(t)"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ 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  -5.79228e-11    0.902311
>         1   0.0995577    0.100186    0.134557    0.455234
>         2   0.0895326   0.0901676    0.126435  0.00815676
>         3   0.0832442   0.0838836    0.123311  0.00541426
>         4   0.0787041   0.0793466    0.117936  0.00376486
>         5   0.0757145   0.0763591    0.116489  0.00198866
>         6   0.0747267   0.0753721    0.112655  0.00177937
>         7   0.0721557   0.0728029    0.109565  0.00255146
>         8   0.0696238   0.0702727    0.107288  0.00241577
>         9   0.0673242   0.0679747    0.106287  0.00157028
>        10   0.0664832   0.0671343    0.104746   0.0014926
>        11    0.064339   0.0649916    0.101947  0.00148105
>        12   0.0635211   0.0641743   0.0991141  0.00131835
>        13   0.0617023   0.0623567    0.101322  0.00147757
>        14    0.060566   0.0612212   0.0965892  0.000719808
> .....................................................................................
> -- 
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