[gmx-users] Protein from the line chain

Justin Lemkul jalemkul at vt.edu
Fri Aug 3 16:51:55 CEST 2012

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


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