[gmx-users] Protein from the line chain

[Justin Lemkul]

On 8/3/12 10:27 AM, Steven Neumann wrote:
> Dear Gmx Users,
>
> I want to simulate protein line chain (80 residues) in explicit
> sovent. Let's assume its axis is x direction. What should be the z and
> y dimension of the box? Is there any rule? Would you wait e.g. for 50

The box size in all dimensions needs to be sufficient to accommodate the protein 
chain in a fully extended configuration aligned with any axis.  You can't 
predict how the protein will rotate, and it is possible (though probably 
unlikely) to rotate 90 degrees in any direction without collapsing at all.  A 
dodecahedral box is your friend here, but a huge amount of atoms is unavoidable.

> ns when it folds and then decrease the simulation box?
>

In doing so, you have to justify your results in the context of a discontinuous 
series of simulations.  Implicit solvent may be a much more advantageous approach.

-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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