On 8/3/12 10:47 AM, Steven Neumann wrote:
On Fri, Aug 3, 2012 at 3:34 PM, Justin Lemkul <jalem...@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
--
========================================
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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