Dear Gromacs Specialists,
I have one problem about g_analyze -ee, May I ask you to help me, Please?
When I do this program as "g_analyze -f .....xvg -av -ee", it is as followed:
Read 4 sets of 83001 points, dt = 6
std. dev. relative deviation of
standard --------- cumulants from those of
set average deviation sqrt(n-1) a Gaussian distribition
cum. 3 cum. 4
SS1 1.811675e+00 1.585145e-02 5.502120e-05 0.416 0.334
SS2 1.476938e+00 5.370597e-02 1.864162e-04 0.011 -0.009
SS3 1.482869e+00 5.208019e-02 1.807730e-04 -0.010 -0.034
SS4 1.475204e+00 5.259068e-02 1.825449e-04 0.012 -0.089
Back Off! I just backed up average.xvg to ./#average.xvg.2#
Set 1: err.est. 0.000400002 a 0.402275 tau1 14.2321 tau2 255.692
Set 2: err.est. 0.002757 a 0.870111 tau1 592.695 tau2 1081.59
Warning: tau2 is longer than the length of the data (498000)
the statistics might be bad
invalid fit: e.e. 0.476411 a 0.999161 tau1 572.985 tau2 2.48396e+10
Will fix tau2 at the total time: 498000
Set 3: err.est. 0.00341541 a 0.998996 tau1 571.479 tau2 498000
Set 4: err.est. 0.00360836 a 0.984581 tau1 578.453 tau2 39087.7
Then, I studied this article: J. Chem. Phys. 116, 209 (2002)
In it has been written " There are restrictions on the range of the fitting
parameters: "a" should be between 0 and 1 and "tau1" and "tau2" should be
larger than 0. When the longest correlation time, "tau2" , is longer than the
averaging interval and "(1-a) tau2" is not negligible compared to "a tau1" ,
there is not enough statistics to estimate the error."
I thought that my problem is related to frequency to write coordinates and the
other outputs to output trajectory file, then I changed it from 200 to 2000 in
md.mdp file, but when I did g_analyze, again I took warning as following:
Read 4 sets of 8001 points, dt = 60
std. dev. relative deviation of
standard --------- cumulants from those of
set average deviation sqrt(n-1) a Gaussian distribition
cum. 3 cum. 4
SS1 1.811686e+00 1.577702e-02 1.763924e-04 0.422 0.376
SS2 1.476945e+00 5.345846e-02 5.976838e-04 0.004 -0.014
SS3 1.482819e+00 5.253597e-02 5.873700e-04 0.002 -0.034
SS4 1.475254e+00 5.289252e-02 5.913564e-04 0.021 -0.084
Back Off! I just backed up average.xvg to ./#average.xvg.1#
Back Off! I just backed up errorgyrate1.xvg to ./#errorgyrate1.xvg.1#
Set 1: err.est. 0.000415045 a 0.741181 tau1 93.389 tau2 374.375
Set 2: err.est. 0.00283072 a 0.964747 tau1 629.293 tau2 1869.63
a fitted parameter is negative
invalid fit: e.e. 0.0025708 a 1.01686 tau1 576.241 tau2 663.907
Will fix tau2 at the total time: 480000
Set 3: err.est. 0.00469726 a 0.997164 tau1 558.935 tau2 480000
Set 4: err.est. 0.00371208 a 0.969329 tau1 551.965 tau2 21102.3
I don't know that where is my mistake and what thing should I change for fix of
this warning!
Please help me.
Best Regards
Dina
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