How to study protein graphene system?

10 October 2016 1 6K Report

I have attached a DNA with graphene sheet. I want to simulate it. Please suggest me the best way to analyze the behavior of the complex system? What should be the best software?

Hiqmet Kamberaj

You may use VMD program for building the graphene sheet and creating the topology file. Then, using either CHARMM or NAMD for performing the molecular dynamics simulations. For adding the topology into the charmm force field topology you may have a look at this thread:

https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=33962

After you perform the simulations you can use VMD or charmm scripting tools to analyze the results.

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