[gmx-users] Adsorption layer of water molecules

Justin Lemkul jalemkul at vt.edu
Thu Feb 7 02:51:31 CET 2013

On 2/6/13 11:56 AM, Yara Alves wrote:
>   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.

This represents a rather small change (something like 3%).  What does your 
analysis of the pressure of the system indicate?

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

Please define what you mean by "spreading."  Can you post links to images?  Why 
would expect discrete adsorption layers in a protein surrounded by water.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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