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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