What are the possible approaches for MD simulation of long RNAs ?

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Martin Klvana

What is the purpose of the simulations?

Kalindu Fernando

Dear Martin Klvana ,

I want to find the intermolecular interactions between peptide and mRNA

Do you need the entire mRNA or would a short fragment suffice?

A short fragment is enough with all four nucleotides. I want to find a way to rationally select a 20-30 oligonucleotide from GFP mRNA.

Thank you !