[gmx-users] Re: Carbon Nanotube Simulation Issues
CS145331 at albany.edu
Tue Jul 24 22:22:04 CEST 2007
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
Thank you again,
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
> 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,
> 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
>> water, at 300k for about 200ps. Also once I accomplish this I wish to
>> either one end of the tube or fix the center of mass position, although
>> 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
>> tried so far. http://cs86.com/CNSE/SWNT.htm
>> Please note all files where created with Vim in the unix environment so
>> think I have eliminated the formatting issues.
>> Also that I have tried the simulation with many different sized tubes
>> (http://turin.nss.udel.edu/research/tubegenonline.html ),
>> both with and without hydrogen capped ends (this is something I have
>> 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
>> file from TubeGen and mainly the residue "UNK" among other things. If
>> one has had luck with using a TubeGen file to create a simulation please
>> me know as to how. Other wise I am looking at a few new options
>> 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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