Hi All,
I want to perform Molecular Dynamics (MD) simulation (using NAMD and CHARMM force field) of carbon nanotube/graphene with topological defect like Stone-wales. Creating topological defects changes the distance among carbon atoms from those using in pristine nanotube/graphene. I wonder whether I have to change the parameters like equilibrium distance and the spring constant value in the topology file or it isn't needed?
If you use a good forcefield, you don't need to do that. Relaxing the system with the defects should give you the changed geometry.
If you want to study the properties of CNT/graphene itself, CHARMM is OK as a first try, but I wouldn't recommend it for an advanced study. It only contain harmonic bonds and angles. You might want to look at something like Tersoff-Brenner. If you want to study the interaction of the defected carbon nanostructure with something else, then CHARMM should suffice.
Hi Mohsan, Thanks a lot for your help. How about topological defects which transform, for example, double bond to triple or even single bond? I assume in this case I have to re-parameterize the structure? changing the spring constant and equilibrium distance,..
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