Hello dear friends
How can I simulate or make a pdb file to simulate graphyne sheet using lammps or atomsk or any other softwares?
Best regards
This is too generic a question. you could as well ask how to do a simulation (anser: read the documentation and text books).
here are some questions to help guide you asking a better question:
- are you talking about graphyne and not graphene?
- are you asking about generating the geometry or how to take an existing geometry and turn it into a LAMMPS simulation?
- do you have any pre-existing experience in MD simulations? if yes, how was this different from what you are trying to do? if no, did you already find a suitable tutor/trainer?
- what kind of simulation are you interested to perform and what do you want to learn from from it?
- do you have already a specific force field in mind?
- did you do some study of the published literature about similar simulations and the same material? if yes, what did you find and where is what you want to do different or did you find it difficult to reproduce? and why, if no, why didn’t you?
axel.
In addition to Axel's questions, I have just one thing to add:
One thing to keep in mind is that regardless which force field you
use, it will be difficult to assemble long carbon chains with
alternating single and triple bonds using traditional molecule builder
tools because most force-fields attempt to infer the bond types (and
angle types, etc) from the atom type alone. And the atom type in the
middle of these long carbon chains is the same. So there's no way for
the molecule builder to know if a bond between a given pair of carbon
atoms should be a single or a triple bond. So my guess is that you
will have to assign the bond types between these atoms in the
acetylene chains manually. (Probably by writing a script to modify a
portion of the data file or .LT file.)
Good luck.
Andrew