[gmx-users] g_analyze -ee

[leila karami]

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?

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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