[gmx-users] hblife

[Mark Abraham]

----- Original Message -----
From: afsaneh maleki <maleki.afsaneh at gmail.com>
Date: Friday, January 29, 2010 1:56
Subject: Re: [gmx-users] hblife
To: jalemkul at vt.edu, Discussion list for GROMACS users <gmx-users at gromacs.org>

> 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    

Axis labels are different from legend labels.

Please cite the full command line, not an abbreviated one. The .xvg shows the full line. Other options can have effects on the output, though it is not clear if/why that might be true here. Try a simple g_hbond -life calculation and see if it differs.

Mark

i send you this file
> 
> Best wishes,
> Afsaneh
> 
> On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul <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 | (540) 231-9080

> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

> 
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