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

liu junjun ljjlp03 at gmail.com
Thu May 26 17:03:08 CEST 2016


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.


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