[gmx-users] [CASS SPAM]Re: How to fix graphite layers?

[Alex]

> First, I multiplied a graphite unit cell in x y z three directions, then cut it to the size I needed, and carefully adjusted the carbon atoms at the edges to conform to the periodic boundary conditions. Therefore, there should be no problem in the way the graphite layers are stacked.
All I meant is that graphite is not a simple stack of graphene sheets 
that are directly above each other (there is a stacking order).
> Second, I dug a spherical hole in the graphite I got in the first step. As a result, each layer of graphite is clearly different. Based on your comments, I should create a top file for each layer of graphite using the x2top command alone. Actually I don't quite understand why I can't create a top file directly for the entire graphite?
In principle, you can. x2top should not assign bonds between atoms 
belonging to separate sheets, just make sure your atomname2type is clean.
> Finally, the main problem I encountered was that the graphite layers were separated from each other during the simulation and could not maintain the original configuration. I don't want to freeze the whole graphite, because then it is non-physical. Is there any way to fix the multi-layer graphite in addition to freezing?
>
That's because either your initial stacking order, and/or interlayer 
distance, and/or individual layer configuration is not compatible with 
the LJ parameters of your carbons (assuming your graphene model is OK) 
-- the result is that the structure falls apart. The way to "fix" things 
is to let the system properly relax instead of masking problems by 
freezing or imposing strong restraints. It is definitely possible in 
Gromacs.

Alex