[gmx-users] Adsorption layer of water molecules

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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