[gmx-users] hblife

[Mark Abraham]

----- Original Message -----
From: Mark Abraham <mark.abraham at anu.edu.au>
Date: Friday, January 29, 2010 2:16
Subject: Re: [gmx-users] hblife
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> 
> 
> ----- 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.

It won't. Now that my brain is turned on, you're just getting what you asked for, which is a frequency plot of H-bond lifetimes. Evidently you have none which persist longer than 14.3ns.

Mark

> 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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