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

高恺 gaokai161 at mails.ucas.ac.cn
Thu Nov 29 09:45:52 CET 2018

Dear Alex:
Thank you very much for your reply.
I am sorry that I did not make my research background clear at first. 
I want to explore the nature of the methane in organic pores in the formations thousands meter underground. 
In order to simplify the problem, graphite is used as a material for the walls of organic pores.
Actually I have written a script that can separate the peripheral atoms (the parts that need to be frozen) from the atoms that are close to the gas. 
My current plan is to divide the two atoms into two groups and set the peripheral atoms to the frozen group in mdp file. I am not sure what the interaction between the frozen and active groups is. If I need to generate top files for each of these two groups, how should I tell the 'hot graphite' to be binded to the frozen graphite adjacent to it?


> -----Original Messages-----
> From: Alex <nedomacho at gmail.com>
> Sent Time: 2018-11-29 16:08:19 (Thursday)
> To: gmx-users at gromacs.org
> Cc: 
> Subject: [CASS SPAM]Re: [gmx-users] [CASS SPAM]Re: [CASS SPAM]Re: How to fix graphite layers?
> > 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.
> Alex
> -- 
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