[gmx-users] Setting up Carbon Nanotube Simulations

Joshua D. Moore jdmoore at unity.ncsu.edu
Thu Nov 29 08:22:32 CET 2007

Dear Bob Johnson and other users,

I am attempting to set up some infinite carbon nanotube simulations.  To
begin, I want to take a single nanotube with some argon inside and try to
simulate it with GROMACS with PBC in the axial direction (it appears I need
to use pbc=full).

So I have a lot of experience with NAMD, but really nothing with GROMACS

So far I can use x2top to generate a topology file from a pdb

It seems to work ok as I can make it output all of the dihedrals and seems
to match up with what I would get with a psf for NAMD.

I am a bit confused on how to include my forcefield with the simulation and
to generate the proper *gro file.  The x2top generated *top file seems to
not have the proper mass for Argon and also doesn't include the parameters
for the forcefield.  I attempted to generate my own forcefield files in the
top directory (ffCNT.itp, ffCNTnb.itp, etc, etc.).  It seems from reading
the mailing list that I don't need to do this and can just use my pdb file
and topology file generated from x2top to start the simulation.

How, then would I include my CNT force field (A morse bond, cosine angle,
and RB dihedral)?  I have created these files already as I stated above.
Could I just include this as a separate *itp file as the methanol example
shows?  Does this file then override the *top file?  So I could include it
as #include "CNT.itp" or something in the *top file?    This is my main
question.  I am also a bit confused on the format of this as I don't really
have a "molecule" as for methanol, just atoms for the carbon and argon

Second question (and very naive).  Can you start a MD simulation with
GROMACS without a *gro file and just a *pdb?

I realize that my message here is a bit naive, so I hoping someone will be
nice enough to overloook my lack of general knowledge about GROMACS :)


Joshua Moore

PS I address Bob Johnson as he seems to be the expert on nanotubes in

Joshua D. Moore
Graduate Student
North Carolina State University
Dept. of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC  27695-7905
Phone: (919) 513-2051
Fax:   (919) 513-2470
Email:  jdmoore at unity.ncsu.edu
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