[gmx-users] freezing graphene sheet

Maryam Kowsar maryam.kowsar at gmail.com
Sat Jul 4 11:39:38 CEST 2015

That's probably because of your forcefield. But if you want to freeze atoms
or groups, you can simply do it by "freeezgrps" and "freezedim" in your
.mdp file. In the former you should assign the groups you want to freeze
and in the latter the directions, eg. 'Y,Y,Y' which means freezing in x,y
and z directions.

On Sat, Jul 4, 2015 at 1:49 PM, Alex <nedomacho at gmail.com> wrote:

> I assume by "deformed" you mean non-flat. Finite graphene flakes in
> vacuum will not stay flat, that's their physics. They also won't be
> exactly flat in a periodic system, or even if you restrain the edge
> atoms, graphene will still be rippled at any nonzero temperature away
> from the edges.
> So, why exactly do you want to "freeze" anything?
> Alex
> GR> Dear all,
> GR> I have simuated graphene and surfactants for 10 ns. When I visualized
> it by
> GR> VMD, I saw that my graphene sheet was deformed. I put graphene finite.
> I am
> GR> trying  to freeze graphene sheet but I am not sure about the my mdp
> file.
> GR> It would be really nice that someone tell me about freezing the
> graphene
> GR> sheet.
> GR> thanks for any suggestion.
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