[gmx-developers] g_energy output compared to g_analyze

hess at sbc.su.se hess at sbc.su.se
Thu Feb 11 09:24:51 CET 2010


I just committed this and sent a mail, I don't recall if that was
to gmx-developers or only to a few developers.
g_energy now uses the exact averages for the error estimation,
but by default it simply uses 5 blocks for the error estimation.
I am considering if to put in the fancier g_analyze error estimation,
(still with the exact sums).

g_energy -h gives the details.


> Hi,
> the development version of g_energy outputs an error estimate:
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> #Surf*SurfTen                267.87        9.9     1551.2   -65.2551
> (kJ/mol)
> Running g_analyze on the otuput xvg file gives:
> SS1   2.757495e+02   1.555144e+03   1.639265e+01      -0.027    0.005
> Back Off! I just backed up /tmp/errest.xvg to /tmp/#errest.xvg.1#
> a fitted parameter is negative
> invalid fit:  e.e. 24.2959  a 1.13429  tau1 0.336301  tau2 1.20464
> Is there a relation between the error estimate in g_energy and in
> g_analyze? I would expect that the same algorithm would be used, or does
> g_energy use the intermediate results that are stored in the edr file in
> a clever way that g_analyze can not?
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> --
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