Dear all,
I am trying to use VMD to generate a graphene structure and output to lammps datafile by topo. It seems there are some bonds missing across the boundaries in the output datafile. Does anyone know how to add bond to the datafile? Thanks!
Dear all,
I am trying to use VMD to generate a graphene structure and output to
lammps datafile by topo.
VMD (and thus topotools) has no integrated facilities to detect/create
bonds across periodic boundaries. PBC support in VMD is extremely limited
in many ways.
It seems there are some bonds missing across the boundaries in the output
datafile. Does anyone know how to add bond to the datafile? Thanks!
most simulations where class 1 force fields (with explicit bonds etc) are
used, graphene or carbon nanotubes are generally left immobile and then
bonds/angles/etc don't matter, or if they are left mobile, people seem to
prefer many-body potentials like Tersoff or AIREBO to represent those
compounds, in which case bonds/angles/etc are implicit and thus *must* not
be included in the data file at all.
axel.
Thank you so much for your reply!
I was following this paper, which gives the graphene C parameters for bond, angle and dihedrals from OPLS AA:
http://www.sciencedirect.com/science/article/pii/S0166516215300057
I will probably keep the graphite rigid as you suggested.
Thank you!
Yafan