[gmx-users] hblife

[Justin A. Lemkul]

afsaneh maleki wrote:
> thanks dear justin'
> 
> it is right that the output of the analysis tools generally writes axis 
> labels and data set legends. in hblife.xyg  file is written that  x 
> axis  label "Time (ps)" and the last time is written 14300.001 whereas 
> my simulated time is 40000 ps not 143000.00 ps   
> i send you this file

It is better to not send attachments, rather cut and paste from your file. 
Sorry, some of us are paranoid about accepting files unless they're specifically 
requested :)

If I recall, the hblife.xvg file should be some sort of probability function, 
p(t) for hydrogen bond half-life.  If it trails off to zero, the file probably 
truncates instead of writing lots of zeroes.

And certainly 14300.001 ps is within the 40000 ps timeframe of your simulation, 
it may just indicate that whatever your analyzing doesn't last terribly long.

You can also use the -ac flag to generate lots of useful information about 
hydrogen bonds, although there are some reproducibility questions that have been 
raised before (see the archives).

-Justin

> 
> Best wishes,
> Afsaneh
> 
> On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     afsaneh maleki wrote:
> 
>         Hi,
> 
>         would you please elaborate the first column in the  hblife.xvg file?
>         hblife.xyg is the output of the following command:
>         g_hbond -life hblife.xvg
>         this column don't show the real time in simulated system.what
>         are these times?
> 
> 
>     Check the headers in the .xvg file; the output of the analysis tools
>     generally writes axis labels and data set legends.  If it still
>     doesn't make sense, post a snippet of your file.
> 
>     -Justin
> 
>         thanks in advance,
>         Afsaneh
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================