network analysis of molecular dynamics trajectories.

[Former user]

Dear Sir, I would like to ask you some questions in the network analysis of molecular dynamics trajectories. I used the tutorial http://thegrantlab.org/bio3d/articles/online/cna_vignette/cna_vignette.spin.html to conduct network analysis on the trajectory, but the number of network graph communities obtained is too large to judge the coupling between them, may I ask Is there any way to improve it?

i am attaching some files for some assistance.

looking forward your response,

[Xinqiu Yao]

Please read the tutorial carefully. There are sections talking about how to manually adjust the number of communities through, e.g., inspecting the modularity and the network.amendment() function. You may also automatically remove ‘isolated’ small communities through the prune.cna() function.

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[wr]

I am very sorry, I just started using Bio3D. Can I use the following code to handle my community network? Why is Cutoff.cij equal to different worth of community maps? The value of cutoff.cij is equal to how much is appropriate, what is the basis for the right? Here is a part of my code. Thanks

cij<-dccm(trj[,inds$xyz])

cm<-cmap(trj[,inds$xyz],dcut=4,scut=0,pcut=0.75,mask.lower=FALSE)

net<-cna(cij,cutoff.cij=0.35,cm=cm)

[wr]

Mr. Yao, can you modify the value of cutoff.cij at will?