Hi Vijayan,
cosine content should say how not-random are the movements observed in
the configuration set you have analized.
Regarding your case, this means that, even if the RMSD is stable
starting from 5ns, the protein still experiences "random" motions.
You should therefore consider as statistically relevant the trajectory
starting from 30ns.
Basing on my experience, I advice you to extend the simulation lenght
(i.e.100ns) to ensure a larger dataset.
Francesco
Il 14/12/2011 00:37, R.S.K.Vijayan ha scritto:
Dear Gromacs users
I have a question regarding cosine content.
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.
But when i perform a cosine content analysis for the eigen vector 1,
i get these strange results
a) Performing a g_analyze run using -b 5000 to -e 50000 ( ie 5- 50 ns
) produces a cosine value of 0.92
but when i perform a cosine analysis using -b 5000 to -e 25000 (
5-25ns) i get a cosine value of 0.24
also when i perform a cosine analysis using -b 30000 to --
50000(30-50 ns) i get a cosine value of 0.05
so how should i interpret this result,
does it imply that all the conformational changes are
taking place between 30 to 50 ns ????
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.
Regards
Vijayan.R
On Mon, Dec 12, 2011 at 5:31 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Alex Jemulin wrote:
Dear all
Which is the difference between hydropilic and hydrophobic sas?
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.
How can give an interpretation to g_sas xvg graph?
Interpretation of the results is based on the question being asked
and the group being analyzed, things that only you know.
What can I find out in it and how can use g_sas to analyze a
trajectory?
Start by reading g_sas -h.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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