[gmx-users] Protein from the line chain

[Steven Neumann]

On Fri, Aug 3, 2012 at 3:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 8/3/12 10:47 AM, Steven Neumann wrote:
>>
>> 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.
>>
>
> Precisely - you run one simulation, obtain a configuration (is it
> representative of the first part of the simulation? randomly chosen?) and
> re-solvate it such that hydration is disrupted unless you take care to
> extract a solvation shell around the protein.  Even then, you can't preserve
> the previous state with respect to thermodynamic observables so it's
> basically a new simulation from some arbitrarily chosen configuration.  If
> you're studying protein folding, that can seem a bit fishy.  In principle,
> there's nothing immediately wrong with doing this, but always be prepared to
> justify your approach.  There are a lot of very tricky questions a reviewer
> can ask if care is not taken.
>
> -Justin
>

Thank you Justin for the clear explanation.

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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