On 2/21/13 8:19 PM, Juliette N. wrote:
Hi Justin,
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
Also :
"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
.xvg"
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?
The .edr file will save specific energy terms at the interval specified by
nstenergy, but it also saves energy history that is accumulated over all frames.
So in reality, .edr files still have knowledge of all MD frames, independent
of what you set as nstenergy. You can only output values every nstenergy frames
for obvious reasons.
-Justin
Please help!
Sorry for naive questions!
On 21 February 2013 19:23, Justin Lemkul <jalem...@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
then
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
identical!
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
.xvg<http://manual.gromacs.**org/online/xvg.html<http://manual.gromacs.org/online/xvg.html>
output
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
etc...
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
description.
-Justin
--
==============================**==========
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Department of Biochemistry
Virginia Tech
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jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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