[gmx-users] block averaging in g_energy vs. g_analyze
Hanne Antila
hanne.antila at aalto.fi
Wed Oct 3 10:25:03 CEST 2012
Dear gurus,
I'm trying to calculate some statistics for the coulomb-sr and
coulomb-recip energies in my system (200 ns simulation). I Suppose the
underlying algorithms in g_energy and g_analyze for making the error
estimate are pretty much the same, but in g_energy the sampling is
more accurate which can cause some differences. However, I'm confused
about two points
1. What can be the cause of nan as g_energy output rmsd when the mean
is ok (and also g_analyze gives ok rmsd)?
2. g_analyze gives me an error regarding set 1. I think this error
implies not-long-enough sampling (longer correlation than run time),
but can there be another cause for this? In this case the correlation
would be very, very long.
I have enclosed the output from g_energy and g_analyze.
All help will be appreciated!
Yours,
Hanne
g_energy:
the last energy frame read 10002 time 200000.000
Statistics over 99984548 steps [ 0.0000 through 200000.0000 ps ], 2 data sets
All statistics are over 16860000 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Coulomb (SR) -1.98611e+06 27 nan 133.058 (kJ/mol)
Coul. recip. -470752 5.7 nan
-18.7256 (kJ/mol)
g_analyze:
Read 2 sets of 10003 points, dt = 19.996
std. dev. relative deviation of
standard --------- cumulants from those of
set average deviation sqrt(n-1) a Gaussian distribition
cum. 3 cum. 4
SS1 -1.986081e+06 2.158308e+03 2.158093e+01 0.003 0.006
SS2 -4.707511e+05 9.907673e+01 9.906682e-01 0.005 0.014
a fitted parameter is negative
invalid fit: e.e. 22.6293 a 1.04171 tau1 14.54 tau2 99.5578
Will fix tau2 at the total time: 200000
Set 1: err.est. 76.0536 a 0.999443 tau1 12.7992 tau2 200000
Set 2: err.est. 6.73835 a 0.926159 tau1 13.7527 tau2 6092.31
gcq#135: "Check Your Input" (D. Van Der Spoel)
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