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 href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
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<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>
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-- <br>
==============================<u></u>==========<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 href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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