normal DNA deforms in simulation

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3 years 8 months ago #4727 by wzhwei173
DNA deforms in simulation was created by wzhwei173
Hello,

I run the simulation of four double strand stiff DNA fragments (using the Version 3 martini DNA) in water, however the DNA deformed a lot and couldn't maintain the helix structure in my simulations. I'd appreciate if anyone can help. Thanks!

You can view the trajectory (vmd 01-em.gro 02-eq.xtc) and all my input files in the following link: Four_DNA_water

Wei

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3 years 8 months ago #4728 by jaakko
Replied by jaakko on topic DNA deforms in simulation
Hi Wei,

sorry this is something we'll put on the DNA tutorial as soon as we get that finished and online. In your .top file the definition of rubber bands needs to be set before including the dna itp file, otherwise the elastic network isn't on.

- Jaakko

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