[gmx-users] Protein from the line chain

[Steven Neumann]

On Fri, Aug 3, 2012 at 3:34 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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


Thank you. What do you mean by discontinuous series of simulations? I
have to use explicit solvent unfortunately. Once it folds in a huge
box I can stop it and place it into the smaller one.

Steven
>
> --
> ========================================
>
> 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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