=12
meV and 
=3.4 A) with a cutoff
potential at 3.2 and a
shifting of the potential in order to have potential continuity at the
cutoff distance.
Carbon nanotube generation
We wrote a Carbon NanoTube GENerator program (
cntgen.c)
to calculate to coordinates of all of the carbon atoms in the tube, and
determine their connectivity. It compiles a table containing all of the
atoms that every atom is bonded to and makes a list of angles from this
table. Finally, the program outputs the data in a format readable by NAMD.
Since NAMD models bonds and angles with straight and angular harmonic springs
of specific rest lengths and rest angles, these connectivity tables are
crucial to the construction of a stable nanotube.
Preliminary study
The potential energy is calculated by a pairwise summation
of a Lennard Jones potentials of the atoms on the first tube and the atoms
on the second tube (with parameter =12
meV and =3.4 A) with a cutoff
potential at 3.2 and a
shifting of the potential in order to have potential continuity at the
cutoff distance.
Input files for NAMD
NAMD takes its input in a specific format (protein file format). The Carbon NanoTube Generation program formats its data into:
- a PDB file where all the atoms are listed
- a PSF file, where we have all of the connectivity,
angles, and (in theory) dihedrals
MD simulation
The molecules were modeled using NAMD, a molecular dynamics program developed by the Theoretical Biophysics Group at the Beckman Institute for Advanced Technology. This code was designed to simulate biomolecular systems and, thus, requires us to input our files in a special format. The input files specify all the positions of the atoms, the connectivity, the bonds parameters, the parameters for non-bonded interaction (ie the Lennard-Jones potential parameters), the constrains applied to the system and the temperature of the simulation.
NAMD interprets the structure by using spring approximations
for bonds and angles. Because the bonds can be seen as springs we
do not need to use periodic boundary conditions or put hydrogen bonds at
the edges of the tubes.
Visualization
The visualization is done by VMD,
also developed by the Theoretical Biophysics Group. In our project, the
VMD visualization program was used for displaying, animating, and analyzing
the output generated by NAMD.
