On Sep 6, 2009, at 5:39 PM, Ragnarok sdf wrote:
I didn´t actually understand what you meant by, "it might be
questionable in regard to its relevance". Is that regarding the
restraint in the Z axis? Would you consider a more "correct"
protocol to slow down even more the pull rate and hope that the "C"
shape does not appear?
Yes. Forcing something to be straight while the conditions make it
bend is
questionable.
XAvier.
Thank you
Fabrício Bracht
On Sep 5, 2009, at 7:42 AM, Ragnarok sdf wrote:
> Hi
> I am trying to calculate the PMF by pulling two membrane protein
> monomers apart using the pull code with umbrella sampling. While
> trying to generate my reaction path, no matter how slow I pull, my
> helix starts bending (not really bending, but it kind of tends to
> transform into a "C" shape inside my bilayer). Since I am only
> simulating a small part of what would a be a very big transmembrane
> receptor, I thought about restraining the movement along the z axis
> of my terminal residues, sort of simulating the "weight" that would
> exist if the entire intracellular and extracellular domains were
> there. My protocol to obtain the PMF is to use this first pulling
> protocol only to generate the different windows (distance between
> the two monomers) in each of which I would use the umbrella sampling
> (maintaining the force constant and switching off the pull_rate) to
> generate data to perform WHAM analysis.
> So that leaves me with two questions.
> First is: would I, by restraining the movement along the Z axis,
> create artifacts that would be computed and ruin my PMF calculation?
Technically speaking, no. But you should correct for the energy of
imposing the
alignment with the z axis.
> And second: Would this be a correct PMF protocol?
That would just give you the PMF of the two transmembrane segments
given their
fixed relative orientations, which might be questionable in regard to
its relevance
but may be not!
It is however strange that you have this C shape even with the slow
pulling.
You might want to check your parameters/procedure. You might need a
long
period of "relaxation/equilibration" to remove the C shape, which
suggests
that you are still pulling too fast!
XAvier.
> Thank you in advance
> Fabrício Bracht
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