I want to perform MD simulation using molecular mechanics force fields. The system consist of SWNT covalently linked with CH3 or COOH groups on the surface. How can I build and setup system for the simulation?
If you are looking for small SWNT, you can use VMD program to generate it. From the main interface, follow the menu "Extensions > Modelling > Nanotube Builder" Once created the structure save the coordinates (ex: swnt.xyz). Open the saved file with Avogadro or AtenProject (visit www.atenproject.net). Then you can easily add CH3 groups to the surface of the NT manually as much as.
I will do as Yusuf said. Do you know which forcefield to employ? I read some papers where OPLS forcefield were employed but I dont know if this is the most suitable one
OPLS (Optimized Potentials for Liquid Simulations) is more useful for aqueous solutions. Lammps has more potentials and it is more suitable for non-biological structures. In this example, one of the reactive type potential energy functions can better describe interactions of connected molecules with nanotube.
https://labs.chem.ucsb.edu/bruice/thomas/tcb_pdf/522.pdf
http://www.sciencedirect.com/science/article/pii/S0927025612000419
Hi,
You can use Materials Studio to build a SWCNT of desired length and type.
Then you can draw the functionalization groups and do the linking as per your requirement.
There are numbers of force fields (COMPASS, UNIVERSAL, DREIDING etc.) available.
Read the attached article
Thanks
Article Molecular dynamics simulation of functionalized SWCNT-polyme...
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