[gmx-users] liquid-solid/liquid-air interface simulations

André Farias de Moura moura at ufscar.br
Fri May 27 04:19:39 CEST 2016

Hi Junjun,

It is possible to cut a rhomboid shape out of hexagonal lattice (I did that
recently to build a graphite substrate). As a matter of fact, it works for
other lattice shapes as well (we've being doing that lately for things as
different as titania, hematite and even a CoO spinel). you just need to
care about the box lengths in each direction, to make sure that periodic
images are located at the correct distance to preserve bond lengths and
angles across the boundaries. I usually use VMD, but there are other
software you might consider (Vesta, Jmol, Avogadro, etc). Depending on the
software you choose, you'll have to dig a little bit in the documentation
to grab the commands ans scripts that need to be used in each case.

periodic boundaries conditions need to be applied in all three directions,
so you have to increase the box length in one of the directions to create a
vacuum region large enough to avoid any interaction between mirror images
of the system in that direction (compressibility needs to be set to zero in
that direction in order to avoid the box being scaled down to suppress the
vacuum region).

You might want to take a look a these papers:

Phys. Chem. Chem. Phys., 2015,17, 3820-3831
Langmuir, 2015, 31 (40), pp 10995–11004
J. Phys. Chem. B, 2005, 109 (9), pp 4032–4041

I hope it helps.


On Thu, May 26, 2016 at 12:03 PM, liu junjun <ljjlp03 at gmail.com> wrote:

> Hello
> I am new to Gromacs and hope to get some suggestions on liquid-solid
> interface as well as liquid-air interface simulations.
> I have two questions:
> 1. how to set up a solid interface from hexaghal crystal unit cell? I
> assume the simulation system need solid to be in a cubic shape so that the
> periodic condition could be applied. But how to convert the hexaghal shape
> to cublic shape for the solid?
> 2. Is it possible to apply the 2D periodic boundary condition? For
> liquid-air interface, the periodic boundary condition should not be applied
> on Z-axes as the gas-phase will be considered just as vacuum.
> It's highly appreciated if there are any suggestions, literature,
> tutorials.
> Junjun
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Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090

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