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Hi Vijayan,<br>
cosine content should say how not-random are the movements observed
in the configuration set you have analized.<br>
Regarding your case, this means that, even if the RMSD is stable
starting from 5ns, the protein still experiences "random" motions. <br>
You should therefore consider as statistically relevant the
trajectory starting from 30ns.<br>
Basing on my experience, I advice you to extend the simulation
lenght (i.e.100ns) to ensure a larger dataset.<br>
<br>
Francesco<br>
<br>
<br>
Il 14/12/2011 00:37, R.S.K.Vijayan ha scritto:
<blockquote
cite="mid:CAMM9PAUNLMkgJVLu=wLpa=T22Ybvc_D3Q+qzk4vWzN4cLD_+KA@mail.gmail.com"
type="cite">Dear Gromacs users
<div><br>
</div>
<div>I have a question regarding cosine content.</div>
<div><br>
</div>
<div>I have a 50 ns trajectory and looking at the RMSD plot, i set
aside the first 5 ns as the time required for stabilization and
subsequently carried out a essential dynamics for the backbone
atoms post 5ns.</div>
<div><br>
</div>
<div> But when i perform a cosine content analysis for
the eigen vector 1, i get these strange results</div>
<div><br>
</div>
<div>a) Performing a g_analyze run using -b 5000 to -e 50000 ( ie
5- 50 ns ) produces a cosine value of 0.92</div>
<div> but when i perform a cosine analysis using -b 5000 to -e
25000 ( 5-25ns) i get a cosine value of 0.24 </div>
<div> also when i perform a cosine analysis using -b 30000 to --
50000(30-50 ns) i get a cosine value of 0.05 </div>
<div> so how should i interpret this result, </div>
<div>does it imply that all the conformational changes are
taking place between 30 to 50 ns ????</div>
<div>or is there some thing wrong with the convergence of the
system??? Papers tell that the cosine value does decreases with
increased time scale due to enhanced sampling, but strange a 25
ns simulation has a low cosine value on the contrary a 50 ns
simulation has an increased cosine value.</div>
<div><br>
</div>
<div>Regards</div>
<div>Vijayan.R</div>
<div><br>
</div>
<div><br>
</div>
<div> </div>
<div><br>
<div class="gmail_quote">On Mon, Dec 12, 2011 at 5:31 PM, Justin
A. Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
<br>
Alex Jemulin wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear all<br>
Which is the difference between hydropilic and
hydrophobic sas?<br>
</blockquote>
<br>
g_sas computes hydrophobic and hydrophilic surface area
based on the absolute value of the partial charge of the
atom, which can be adjusted with the -qmax flag.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
How can give an interpretation to g_sas xvg graph?<br>
</blockquote>
<br>
Interpretation of the results is based on the question being
asked and the group being analyzed, things that only you
know.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
What can I find out in it and how can use g_sas to analyze
a trajectory?<br>
<br>
</blockquote>
<br>
Start by reading g_sas -h.<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | <a moz-do-not-send="true"
href="tel:%28540%29%20231-9080" value="+15402319080"
target="_blank">(540) 231-9080</a><br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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