[gmx-users] problem with nanotubes and vitamin simulation

Naga Rajesh Tummala rajesh.tnr at gmail.com
Wed Sep 2 20:43:09 CEST 2009

Dear Gromacs Users,

I am using GROMACS to run simulations of flavin mono nucleotide around
carbon nanotubes.

During first 10 ns I keep nanotubes rigid, and nanotubes contain carbon
atoms fixed to their positions.
After 10 ns , I change the nanotube type from just composed of fixed carbon
atoms to a single rigid body (with each carbon atom bonded to three other
carbons within nanotube )
(I also insert atoms along the nanotube axis and are bonded to atoms on the
surface of the nanotube, essentially to keep the nanotube cylindrical. All
the bonds are modeled using harmonic potential)

I am studying the PMF of 2 carbon nanotubes as a function of distance
between them, using simplified model for CNTs. I was able to use this method
when I had sodium dodecyl sulfate, water, CNTs in the system. When I try to
use this with flavin mono nucleotide, I run into problems. As long as CNTs
are just fixed carbon atoms, the simulations work fine. As soon as I change
the CNT to a rigid body (with position as before) with a different atom
type, the segmentation fault occurs when I run the simulation.

For some strange reason, the LJ -SR energies are too repulsive (oder of e18,
where as they are order of e-5 when CNT is not a single rigid body). I went
through the .tpr file and found that the pair LJ values generated are right.
I wrote a separate fortran code and found that there are no atoms separated
by less than 0.3 nm.

I spent almost a week trying all different combinations I can think of. I
will greatly appreciate if anyone of you can reason such strange behavior.

input, topol, initial configuration, force field files for both the
simulations (one that works with CNT composed of carbon atoms, CNT as single
rigid body) are attached.
I had sent another mail with all the attached files, but that is awaiting
moderator approval because of the size of the mail. I will be glad to send
those files to anyone interested)

Thanks a lot

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