Dear Justin, The initial configuration for this simulation is the configuration obtained from 10 ns of simulation. The only thing that is changed is that I now consider a nanotube as a single rigid body connected by bonds, so that I can make the nanotube move along the x-direction as a whole.
I did write a small FORTRAN code to check for atomic overlap (especially between FMN and CNT, FMN-CMT , SOD-CNT, SOD-CMT). I could not find any atomic pair less than 0.3 nm. Thanks Rajesh
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