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On 1/12/2010 8:25 PM, vinothkumar mohanakrishnan wrote:
<blockquote
cite="mid:AANLkTinSNWBVAv5=pf8jhxUdO+1ed-AZfZf4PthS1aiT@mail.gmail.com"
type="cite">Dear Mark<br>
<br>
Thank you for your explaination but Its not clear to me what you
are trying to say. can you explain it bit more clearly. what
should i need to do to get the standard error? any help is highly
appreciated.<br>
</blockquote>
<br>
Like I said, you need to make independent measurements of a quantity
to form an estimate of the mean, and thus an estimate of the
standard deviation among such estimates (i.e. standard error of the
mean). This is pretty basic scientific statistics. Your MD steps are
all correlated because of how they were generated, so you need to
look at the autocorrelation time (Google!) of your observable to get
a starting idea of how many actual independent measurements your
data represents.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTinSNWBVAv5=pf8jhxUdO+1ed-AZfZf4PthS1aiT@mail.gmail.com"
type="cite">
<br>
Regards<br>
Vinoth<br>
<br>
<div class="gmail_quote">On Wed, Dec 1, 2010 at 2:39 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div>
<div class="h5">On 1/12/2010 7:59 PM, vinothkumar
mohanakrishnan wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Hi Gromacians<br>
<br>
I am planning to compute the standard error for the
interfacial surface tension of water-dichloro ethane. i
just want to know is my procedure right. below is the
result what i get from my g_energy command.<br>
<br>
Statistics over 500001 steps [ 0.0000 thru 1000.0001 ps
], 1 data sets<br>
All averages are exact over 500001 steps<br>
<br>
Energy Average RMSD
Fluct. Drift Tot-Drift<br>
-------------------------------------------------------------------------------<br>
#Surf*SurfTen 692.904 4579.46
4579.16 -0.181601 -181.602<br>
<br>
my question is to calculate the standard error should i
need to divide the RMSD(4579.46) by the squareroot of
500001 steps? any help is highly appreciated.<br>
</blockquote>
<br>
</div>
</div>
Calculating the standard error of the mean in this way
requires that the observations are independent (<a
moz-do-not-send="true"
href="http://en.wikipedia.org/wiki/Standard_error_%28statistics%29"
target="_blank">http://en.wikipedia.org/wiki/Standard_error_%28statistics%29</a>).
Adjacent MD frames are not. You would need to know something
about your correlation times to know how long you have to wait
before effective independence.<br>
<br>
Mark<br>
<font color="#888888">
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