[gmx-users] simulating films at air-water interface

[Andre Farias de Moura]

dear all,

I just began to study the formation of self-assembled
molecular films of a semi-conductor organic dye at the
air-water interface.

to begin with, I replicated spc216.gro to achieve the
desired water layer thickness, then I added the organic
layer below and above and reseted the simulation box edge
along the z direction to 50.0 nm, producing an evacuated
region between periodic images. Although I've specified
the removal of center of mass motion every time step, the
whole system is moving upward in the z direction. That
possibly means that some molecular kinetic energy is
being converted into COM kinetic energy and that will
introduce some artifacts in the structural and dynamical
properties of the system.

any suggestions on the way to simulate such system without
this kind of error?

thanks in advance,

Andre'

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    Dr. Andre' Farias de Moura
     Grupo de Quimica Quantica
Instituto de Quimica de Sao Carlos
     Universidade de Sao Paulo
        Sao Carlos - Brasil
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