[gmx-users] Setting up Carbon Nanotube Simulations

[Robert Johnson]

Hi Joshua,
Since each carbon-carbon bond is identical, you can just include the
bonded information as a separate .itp file or at the top of your
system .top file. For example, at the top of your .top file you can
include the [ defaults ], [ atomtypes ], [ bondtypes ], [angletypes],
[dihedraltypes], [moleculetypes] before the [ atoms ] section. You can
then include the force field parameters in these sections. Check the
Gromacs manual for the proper syntax. One note of caution. The
function types in the  [ bonds ] and [ bondtypes ] sections (same for
angles etc.) must match.  Thus, even though you will have the
parameters left blank in the [ bonds ] section, if you are using a
Morse potential you have to make sure that there is a 3 for function
type.

If you opted to use a separate .itp file, you would have to place all
the [ *types ] sections in a separate file. You would then generate
separate .itp files for each molecule you are working with (nanotube
and argon). Then you would have a master topology file .top that
includes all the necessary files and specifies how many of each are in
your system.

All you need to start a Gromacs simulation is an input file (.mdp), a
topology file and a coordinate file. The format of the coordinate file
can be anything (.pdb, .gro, .g96 etc.)
Bob





On Nov 29, 2007 2:22 AM, Joshua D. Moore <jdmoore at unity.ncsu.edu> wrote:
> 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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