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

[高恺]

Dear Alex:
Thank you very much for your patience and detailed response. 
I seriously considered each of your comments and re-checked my configuration.


> 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).

Maybe you are talking about the polytypism of minerals. I checked the mineralogy textbook, and graphite has two types: 2H and 3R. The 2H type stack is used in my simulation.

> 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.

I re-checked the initial configuration： 
The interlayer distance is 0.34nm， which is consistent with other data descriptions.

I also run some simulations last night:
After removing the gas in the system, both the graphite block composed of complete sheet and that with a spherical hole inside(I implemented it by removing some of the carbon atoms on each sheet) can maintain the initial configuration. This shows that the graphite configuration used in the simulation should be OK.
I think it is the high pressure of the gas in the pore that separates the graphite sheets from each other. Considering that my experimental background is deep in the earth, there should be enough pressure to keep the graphite intact.
So I want to know: In gromacs, if there is a way to prevent graphite from being blown up by high pressure gas. I am worried that using strong restraints make the simulation results unreliable.

Can you give some advice?

Thank you again for your kind reply!

Kevin

> -----Original Messages-----
> From: Alex <nedomacho at gmail.com>
> Sent Time: 2018-11-28 17:06:02 (Wednesday)
> To: gmx-users at gromacs.org
> Cc: 
> Subject: [CASS SPAM]Re: [gmx-users] [CASS SPAM]Re: How to fix graphite layers?
> 
> 
> > 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
> -- 
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