[gmx-users] Setting up Carbon Nanotube Simulations

[Joshua D. Moore]

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
atoms.

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 :)

Thanks

Joshua Moore

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

-- 
------------------------------------------------
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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