Molecular dynamics simulation of single walled-carbon nanotubes (SWCNTs) using GROMACS: Comparison of water models

Single-walled carbon nanotubes (SWCNTs) have attracted great interest due to their intrinsic electrical and mechanical properties [1] as well as their potential applications in various areas such as electronics, biosensors and drug delivery. Due to the high price of pure carbon nanotubes (CNTs) for performing the experimental efforts, computational studies of these useful and applicable compounds is highly sought.Molecular dynamics (MD) simulation as a powerful computational method can be used to consider the dynamics and treatment of CNTs separately or in interaction with biomolecules. MD studies showed that SWCNTs could act as hydrophobic channels for conduction of water molecules [2]. There are some studies on MD simulation of carbon nanotubes in interaction with peptides using software packages such as AMBER and CHARMM [3, 4]. Nevertheless, we have not found much research regarding simulation of CNTs using GROMACS as a free and powerful MD simulation software package.In this research, we have performed molecular dynamics simulation of SWCNTs using GROMACS in order to investigate the influence of two different water models of SPC and TIP3P on the potential energy of CNTs. This study helps us to find the best model affected on the simulation of CNTs for further studies in aspect of interaction of these materials with biomolecules