[gmx-users] weird mdrun...using gromacs 3.3.3

Naga Rajesh Tummala rajesh.tnr at gmail.com
Tue Sep 8 19:08:00 CEST 2009

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.

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