[gmx-users] g_analyze -ee

[dina dusti]

Dear Justin,

Thank you very much from your response.

Best Regards
Dina



________________________________
 From: Justin A. Lemkul <jalemkul at vt.edu>
To: dina dusti <dinadusti at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Monday, February 20, 2012 11:07 PM
Subject: Re: [gmx-users] g_analyze -ee
 


dina dusti wrote:
> Dear Justin,
> 
> Thank you very much from your response.
> OK, but is it important? Because these warnings are appeared some where, not for all of calculations. For example, these are appeared for gyrate.xvg and not for moment.xvg!
> 

The warnings indicate that the error estimates are not reliable.  It's all to do with the autocorrelation time.  Some quantities converge faster than others. The appendix of the cited paper in g_analyze -h explains the entire derivation and what each term means.

-Justin

> Thank you again from your help and excuse me from my delay for thank from you.
> 
> Best Regards
> Dina
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* dina dusti <dinadusti at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Saturday, February 18, 2012 5:29 PM
> *Subject:* Re: [gmx-users] g_analyze -ee
> 
> 
> 
> dina dusti wrote:
>  > Dear Gromacs Specialists,
>  >
>  > Sometimes, when I do "g_analyze -f      .xvg -av -ee error.xvg" , I take following warning, and I don't know how to fix it.
>  >
>  > Set  1:  err.est. 0.000596502  a 0.29217  tau1 24.8856  tau2 443.641
>  > Warning: tau2 is longer than the length of the data (864000)
>  >          the statistics might be bad
>  > invalid fit:  e.e. 0.285911  a 0.995985  tau1 1434.16  tau2 1.41932e+09
>  > Will fix tau2 at the total time: 864000
>  > Set  2:  err.est. 0.00859257  a 0.995692  tau1 1432.7  tau2 864000
>  > Set  3:  err.est. 0.00527967  a 0.588024  tau1 804.83  tau2 3603.55
>  > a fitted parameter is negative
>  > invalid fit:  e.e. 0.00421461  a 1.08722  tau1 1672.3  tau2 6955.25
>  > Will fix tau2 at the total time: 864000
>  > a fitted parameter is negative
>  > invalid fit:  e.e. -nan  a 1.00449  tau1 1455.53  tau2 864000
>  > Will use a single exponential fit for set 4
>  > Set  4:  err.est. 0.00453113  a 1  tau1 1400.34  tau2 0
>  >
>  > Please help me.
>  > Thanks in advance from your response.
>  >
> 
> It likely means the data are poorly converged.  Refer to the paper cited in g_analyze -h regarding the error calculation for details and a complete description of the error estimate method.
> 
> -Justin
> 
> -- ========================================
> 
> 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
> 
> ========================================
> 
> 

-- ========================================

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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