From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Sat Aug 11 2007 - 01:33:01 CDT
Hi,
I am attempting to simulate flexible infinitely long nanotubes with NAMD.
When I apply the periodic boundary condition in the axis direction, I find
that the ends don't seem to be connected. They sort of bunch up. I believe
this is a problem with the periodic boundaries, but I am not sure. So my
question is really, can I do this with NAMD and if so, how should I choose
my axial unit cell vector?
I haven't found anything in the mailing lists that point to the answer.
There was a previous question very much related to this from November 2006,
but it didn't appear to be answered on the list at least. It seems that
people are able to do this, but with GROMACS.
When I visualize the nanotube in VMD and apply my axial direction unit cell
vector to see the images, they seem to align properly. There is a gap
between the images, but I thought that this was correct as this gap accounts
for the bond length between the carbon atoms in the images. If I choose the
periodic boundary so that the end atoms overlap each other, I still get
problems, because I am guessing the atoms are overlapping!
I am hoping that someone with more experience with tubes or carbon nanotubes
has some advice. I am including an example with the files located at the
following address (psf, pdb, conf, and parameter files):
http://chumba.che.ncsu.edu/users/joshua/nanotube_example/
My example there is a (16,16) armchair nanotube with some argon atoms inside
with the periodic z unit cell (0 0 48.806).
Now that I have experimented quite a bit, I don't see how the bonds
between the images can be included at all. I could add bonds between the
end atoms on each side of the nanotube to my *psf file manually, but I am
not sure if this is the solution. I am not sure, but I really think that
this is the problem..... the end atoms don't know that they are bonded to
anything so they are free to move.
Thanks in advance.
Joshua Moore
-- ------------------------------------------------ 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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