[gmx-users] How to fix graphite layers?
nedomacho at gmail.com
Wed Nov 28 04:50:38 CET 2018
If the layers are not identical, use x2top on each layer separately,
combine all layers properly in graphitic stacking order, add topologies нas
needed. If the layers are identical, use x2top only on one, then repeat as
It is important how the layers are stacked and how they interact, otherwise
the simulation is garbage.
On Tue, Nov 27, 2018, 8:40 PM 高恺 <gaokai161 at mails.ucas.ac.cn wrote:
> Dear all:
> I am currently working on a graphite hole filled with methane. I generate
> my top file by using g_x2top and it works well when there is only one layer
> of graphene.
> But when I use multi-layer graphite, these layers often spread out because
> of insufficient interlayer force. My simulation does not care about the
> mechanical properties of graphite, so I hope that graphite can maintain its
> initial shape.
> I have tried position restraints and the top file looks like:
> [ moleculetype ]
> ; Name nrexcl
> GRA 1
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> 1 C2 1 GRA C2 1 0
> 2 C2 1 GRA C2 2 0
> 79586 C2 1 GRA C2 79586 0
> [ positon_restraints ]
> 1 1 5000 5000 5000
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 5 1 1.420000e-01 5.857600e+05 1.420000e-01 5.857600e+05
> 1 6 1 1.420000e-01 5.857600e+05 1.420000e-01 5.857600e+05
> [ system ]
> [ molecules ]
> GRA 1
> Methane 3500
> But it doesn’t seem to work, the graphite molecular layers will still
> I am also considering freezing a portion of the graphite and keeping the
> graphite in contact with the gas active. Is this feasible? Is there any
> other way to fix the initial shape of the graphite while keeping it at a
> temperature similar to that of a gas?
> I would be grateful if anyone could help me.
> Kevin Gao
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