Re: [gmx-users] g_analyze -ee

2012-02-20 Thread Justin A. Lemkul 



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 jalem...@vt.edu
*To:* dina dusti dinadu...@yahoo.com; Discussion list for GROMACS 
users gmx-users@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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Re: [gmx-users] g_analyze -ee

2011-12-29 Thread Mark Abraham 

On 30/12/2011 1:06 AM, leila karami wrote:

Dear gromacs users

I want to calculate error estimates using block averaging for output 
from g-dist

(distance between donor atom of protein and acceptor atom of dna).

I used g_analyze -f dist.xvg -ee

there are 3 columns in output file.

anyone give me more explain about these columns?


Have you read g_analyze -h and perhaps consulted the reference you can 
find there?


Mark



how to explicate and interpret these data?


In the one of the my output files, I encountered

Read 1 sets of 1252 points, dt = 0.0119951

   std. dev.relative deviation of

standard   -   cumulants from those of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
   cum. 3   cum. 4

SS1   7.918456e+00   2.788148e+00   7.882919e-02  -0.717   -0.202


Back Off! I just backed up e11grey.xvg to ./#e11grey.xvg.2#
Warning: tau2 is longer than the length of the data (15.0059)
  the statistics might be bad

invalid fit:  e.e. nan  a 2.07331  tau1 3.99138  tau2 183052
Will fix tau2 at the total time: 15.0059
a fitted parameter is negative
invalid fit:  e.e. nan  a 16.5523  tau1 10.8852  tau2 15.0059
Will use a single exponential fit for set 1

Set   1:  err.est. 1.26673  a 1  tau1 1.54994  tau2 0

how to fix that?

Best regards





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