[gmx-users] Re: Carbon Nanotube Simulation Issues

[Robert Johnson]

Hi Chris,
You will have to pick the force field you want to use and include that
information after you generate the topology file. You can leave out
the force field parameters in your topology file. You can then add
these parameters in [ bondtypes ], [ angletypes ] and [ dihedraltypes
] sections (check out the Gromacs manual topology section). Check out
the literature to see what force field parameters they are using.
Bob


On 7/24/07, Christopher Stiles <CS145331 at albany.edu> wrote:
>
>
>
>
> Hi Bob,
>
>      Thank you so much for the quick and detailed response. I am looking to
> simulate a finite CNT. I do have one point of clarification though, when you
> say you will have to add in the force field parameters afterwards, does this
> mean I must pick the force field I wish to use after wards and manually put
> that in or are your referring to the Residue (in the *.pdb file it is
> "UNK").
>
>
>
> Thank you again,
>
>
>
> ~Christopher Stiles
>
> College of Nanoscale Science and Engineering (CNSE)
>
> State University of New York, Albany, New York 12203, USA
>
>
>
>
> > Hi Chris,
>
> > Can you visualize your nanotube coordinates with a program like VMD to
>
> > make sure that it looks ok? However, I'd assume your coordinate file
>
> > is just fine.
>
> >
>
> > First off, do you want to simulate a finite nanotube or an infinite
>
> > nanotube?
>
> >
>
> > If you want an infinite nanotube do this:
>
> > 1) Orient nanotube along z-axis (probably this is already done)
>
> > 2) Determine the length L of the nanotube
>
> > 3) Generate a box around your nanotube coordinates with a z-dimension
>
> > equal to L+b. Here, b is the amount of extra space needed to make your
>
> > nanotube to be periodic. Use this command: editconf -f nt-coords.pdb
>
> > -o nt-box.pdb -c -box 10 10 <L+b>
>
> > 4) Generate topology with this comand: x2top -f nt-box.pdb -o
>
> > nt-infinite.top -pbc -ff gmx
>
> > This will generate a topology with definitions for the bonds, angles
>
> > and dihedrals. You will have to edit this file to include the force
>
> > field parameters for each of these interactions. However, since every
>
> > single atom in your nanotube is the same, the interactions all have
>
> > the same parameters.
>
> >
>
> > If you want a finite nanotube that is capped with hydrogens you should
>
> > use this command:
>
> > x2top -f nt.pdb -o nt.top -ff gmx
>
> >
>
> > Again, you will have to add in the force field parameters afterwards.
>
> > However, this is trivial since all the interactions are identical.
>
> > Good luck,
>
> > Bob
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> > On 7/24/07, Christopher Stiles <CS145331 at albany.edu
>
>
> > <http://www.gromacs.org/mailman/listinfo/gmx-users> >
> wrote:
>
> >>
>
> >>
>
> >>
>
> >>
>
> >> I am trying to simulate a single wall carbon nanotube in a box solvated
>
> >> in
>
> >> water, at 300k for about 200ps. Also once I accomplish this I wish to
>
> >> fix
>
> >> either one end of the tube or fix the center of mass position, although
>
> > this
>
> >> part is unimportant if I can not get the thing to run at all yet.
>
> >>
>
> >>
>
> >>
>
> >> I have created a page with a full detailed account of what I have done
>
> >> and
>
> >> tried so far. http://cs86.com/CNSE/SWNT.htm
>
> >>
>
> >> Please note all files where created with Vim in the unix environment so
>
> >> I
>
> >> think I have eliminated the formatting issues.
>
> >>
>
> >> Also that I have tried the simulation with many different sized tubes
>
> >> from
>
> >> TubeGen
>
> >> (http://turin.nss.udel.edu/research/tubegenonline.html
> ),
>
> >> both with and without hydrogen capped ends (this is something I have
>
> >> read
>
> > in
>
> >> the archives as a possible solution, it makes no difference in the end).
>
> >>
>
> >>
>
> >>
>
> >> I have come to the conclusion through the help of many of you that the
>
> > *.pdb
>
> >> file from TubeGen and mainly the residue "UNK" among other things. If
>
> >> any
>
> >> one has had luck with using a TubeGen file to create a simulation please
>
> > let
>
> >> me know as to how. Other wise I am looking at a few new options
>
> >> basically
>
> >> all of them involve writing my own files.
>
> >>
>
> >>
>
> >>
>
> >> I guess I am looking for advice where to go from here.
>
> >>
>
> >>   ~Christopher Stiles
>
> >> College of Nanoscale Science and Engineering (CNSE)
>
> >> State University of New York, Albany, New York 12203, USA
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