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

[高恺]

Dear Alex:

Thank you very much for your reply, but I think I may not have expressed my doubts.

First, I multiplied a graphite unit cell in x y z three directions, then cut it to the size I needed, and carefully adjusted the carbon atoms at the edges to conform to the periodic boundary conditions. Therefore, there should be no problem in the way the graphite layers are stacked.

Second, I dug a spherical hole in the graphite I got in the first step. As a result, each layer of graphite is clearly different. Based on your comments, I should create a top file for each layer of graphite using the x2top command alone. Actually I don't quite understand why I can't create a top file directly for the entire graphite?

Finally, the main problem I encountered was that the graphite layers were separated from each other during the simulation and could not maintain the original configuration. I don't want to freeze the whole graphite, because then it is non-physical. Is there any way to fix the multi-layer graphite in addition to freezing?

Thank you again for your reply!

Kevin

> -----Original Messages-----
> From: Alex <nedomacho at gmail.com>
> Sent Time: 2018-11-28 11:50:20 (Wednesday)
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Cc: 
> Subject: [CASS SPAM]Re: [gmx-users] How to fix graphite layers?
> 
> 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
> above.
> 
> It is important how the layers are stacked and how they interact, otherwise
> the simulation is garbage.
> 
> Alex
> 
> 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
> >  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 ]
> > GRA+Methane
> >
> > [ 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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