Safron,
I just wrote a little tutorial for some students to create a lammps data file and .psf file for a nanotube on graphene starting from an xyz file. The starting system was created using Nanoengineer2. I used Axel’s topotools webpage (referenced in the pdf file) as a starting point. His page is very helpful.
I assume you want to use charmm or similar potential to describe the interactions. Alternatively you could just use airebo or tersoff and not worry about the angles at all.
Files attached:
c5x5…xyz (the starting file)
test.dat (the resulting lammps data file)
test.psf (the resulting psf file)
in.test (a lammps input script that will run a simulation of the test.dat.
makingpsffile.pdf - the howto.
Please note that the bond, angle, and dihedral parameters in the in.test file are just something that I threw together to get the simulation working. They may or may not be the most ideal set of parameters. User be warned!
in.test (1.74 KB)
test.psf (879 KB)
test.dat (691 KB)
5x5CNTonGraphene.xyz (124 KB)
makingpsffile.pdf (174 KB)