[gmx-users] Statistical uncertainty in gromacs
joojoojooon at gmail.com
Fri Feb 22 02:19:51 CET 2013
When one issues g_energy –f *.edr –nmol X –b XXX, g_energy reads the frames
from -f edr. file which is already written each nstenergy = 1000 steps for
instance. So g_energy is not reading all MD steps. and I guess the same
steps are printed to .xvg as out of g_energy. Please help me realize why
g_energy is more accurate. I am confused :( Where are these all MD steps
written that is stated in g_energy - h
"that in most cases the* energy files contains averages over all MD*
steps, or over many more points than the number of frames in energy file*.
This makes the g_energy statistics output more accurate than the
By energy file we mean .edr file, right?
Why does it say *energy file* contain averages over all MD ...than the
number of frames in *energy file*?!
I am not able to differentiate between energy file and energy file?
Sorry for naive questions!
On 21 February 2013 19:23, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 2/21/13 6:58 PM, Juliette N. wrote:
>> Hi Matthew,
>> Thanks for your reply. I tried g_analyze as you suggested:
>> 1) I am wondering why the average given by g_energy and g_analyze are not
>> identical. I tried the following:
>> g_energy -f Potential. edr -o Potential.xvg and extracted the average
>> provided Potential.xvg as input to g_analyze ( I did this since g_analyze
>> seems to read xvg files only). and issued: g_analyze –f.Potential.xvg–av.
>> However the averages are not identical.
>> 2) Also I tried g_energy -f Potential. edr -o Potential.xvg and from
>> g_energy I can see Energy Average *Err.Est.*
>> RMSD Tot-Drift
>> are given by default. Then tried g_analyze -ee and noticed that the *
>> Err.Est.* reported by g_energy and the one from g_analyze -ee are not
> See the message below, printed by g_energy.
>> Could you please explain why is this happening and how *Err.Est.* is
>> estimated? .
>> g_energy says:
>> An error estimate of the average is given based on a block averages over 5
>> blocks using the full-precision averages. The error estimate can be
>> performed over multiple block lengths with the options -nbmin and -nbmax.
> The following section explains the discrepancy in your results:
> Note* that in most cases the energy files contains averages over all MD
>> steps, or over many more points than the number of frames in energy file.
>> This makes the g_energy statistics output more accurate than the
> Thus, the only way to achieve absolute agreement between .xvg and .edr
> analysis is to set nstenergy = 1, which will result in really big .edr
> files, and the difference in practice should be pretty small.
> I cant seem to understand how error is obtained.:( If I am reading the
>> frames from say , -b 4000 -5000, what happens if I dont provide blocks
> Well, there are default values that are used for -nbmin and -nbmax, so if
> you don't specify any values manually, those are used. The default is 5.
> Without looking into the code, it would seem that block averaging of some
> sort is being done. The error estimate for g_analyze -ee is documented
> more thoroughly and is described in the paper mentioned in the help
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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