[gmx-users] Adsorption layer of water molecules

Yara Alves yarapalves at gmail.com
Wed Feb 6 17:56:56 CET 2013

 I'm working with a protein in water and I used periodic boundary conditions
in three dimension.
At first the initial system was minimized, then I followed Justin's
protocol. The system was equilibrated in a first stage nvt for 1 ns and in a
second stage npt for 1 ns (with restraints).
Then the production stage had been done with 100ns.

When I visualize the trajectory results in vmd, I have a problem with the
adsorption layer. During the production trajectory, water molecules had
spread very much and actually no adsorption happened.
The size of the box increases a lot in the beginning of the pvt equilibrated
stage (it was 341 nm³ and it becomes 351nm³) and I can't understand that.

Why are the water molecules spreading so much? Why don't they constitute an
adsorption layer?

Any help would be appreciated.

*Yara Pereira Cerceau Alves*
Graduanda em Engenharia de Alimentos
Bolsista PIBIC/CNPq
Universidade Federal de Viçosa - UFV/MG

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