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

Alex nedomacho at gmail.com
Thu Nov 29 09:08:16 CET 2018

> I re-checked the initial configuration:
> The interlayer distance is 0.34nm, which is consistent with other data descriptions.
That is the interlayer distance that corresponds to the experimental 
data for HOPG graphite. Whether it is compatible with the LJ parameters 
of your carbons is a completely separate issue. If the difference is 
unclear, I will not be able to help further, sorry.
> 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.
I am not sure what your system is and why there is gas, and why its 
pressure is splitting your graphite. In any case, if you need to apply 
restraints, you don't have to apply them to the entire sheets. You can 
always apply them to the perimeter of each sheet, some sort of script 
that reads the coordinates and spits out the list of restrained atoms 
along the perimeter (within some selected width) would be useful. It 
will keep the sheets together and also completely mask the fact that 
your system explodes due to instability.


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