Hi,
I am going to perform MD simulation for the Nanoporous Graphen sheet. I know how to make the pores in VMD. But when I tried to make the data file it was lacking a lot of parameters such as angles masses,..etc !!
so what exactly I need is to build a system such as shown in the figure attached.
where that the potential used for graphene sheets is the AIREBO potential.
I would appreciate anyone could help and show me what steps to follow.
There are various ways to construct a system either in VMD, in LAMMPS itself, or for example coding some script by yourself.
When using VMD, you might want to look into TopoTools, which enables you to do a bunch of things including assigning bonds, angles, dihedrals, and impropers (the latter two you won't need I guess) and write a LAMMPS data file.
In the command window in VMD or in a script you can use the following commands
topo guessbonds
topo guessangles
topo writelammpsdata test.data
This is not a step-by-step manual of how to build your system, but hopefully it helps.
Please take a look at the following links:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-1
Furthermore, you should be careful with the forcefield type. Classical forcefield needs to have molecular properties such as bond, angle, etc. in the data file.
While some others like AIREBO forcefield are atomic style and requires different data structure in the data files.
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