Re: [gmx-users] PMF and pull with membrane helix

[XAvier Periole]

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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