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I have just started working with VMD, and I figured out how to generate a Carbon Nano Tube (CNT) in VMD and save it's atom positions to use as initial file in LAMMPS. My question is, if you know of any simple way in VMD so that I can get the bonding and angle data as well, to use in my LAMMPS initial file?

in other words, after creating a CNT in VMD, How can I generate a data file containing not only the atom positions, but also bonding and angle information in the format of LAMMPS initial input file?

Best Regards

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2 Answers 2

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Use Tkconsole under extension and follow

topo retypebonds
topo guessdihedrals
topo writelammpsdata lmp.data full

enter image description here

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  • $\begingroup$ Thank you so much, Do you know of anyway I can create a diffent nanotube rather than Hegzagonal lattice in VMD? I mean is there any way I can change the lattice to whatever I want? $\endgroup$ Commented Feb 14, 2022 at 17:33
  • $\begingroup$ Since I can easily get the input file for LAMMPS from VMD, I 'm looking for away to generate my own lattice shape like for example triangular lattice nanotube. Is that possible? $\endgroup$ Commented Feb 14, 2022 at 17:37
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    $\begingroup$ @DelaramNematollahi kindly create a new question in forum regarding triangular nanotube $\endgroup$ Commented Feb 15, 2022 at 2:34
  • $\begingroup$ Hi I did that here is the link thank a lot: mattermodeling.stackexchange.com/questions/8690/… $\endgroup$ Commented Feb 15, 2022 at 15:25
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If you like me prefer working in the python ecosystem, I suggest using lammps-interface and Atomic Simulation Environment (ASE).

lammps-interface is a python code that interfaces crystal structures in cif format to lammps input files.

It is easy to install and use, simply pip install it and run:

lammps-interface cif_file.cif

By default, this gives you the input files for the Universal Force Field (UFF). There are a few other options, including the Dreiding force field.

If you want to convert your crystal structure to cif format, use Atomic Simulation Environment (ASE).

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