Naga Rajesh Tummala wrote:

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.


Can you post the relevant .mdp file(s)? Are you preserving velocity information from the previous trajectory, or generating new velocities? Are any of the species in your system constrained?

-Justin

Thanks
Rajesh




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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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