[gmx-users] Cosine content

[Francesco Oteri]

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 <jalemkul at vt.edu 
> <mailto:jalemkul at 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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