[gmx-users] How to fix graphite layers?

[Alex]

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.