[gmx-users] How to fix graphite layers?

高恺 gaokai161 at mails.ucas.ac.cn
Wed Nov 28 04:40:17 CET 2018

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         12.011
     2        C2       1          GRA      C2         2        0         12.011
79586       C2       1          GRA      C2       79586        0         12.011

 [ 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 spread.

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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