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