<div class="gmail_quote"><div>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? <br>
Thank you<br>Fabrício Bracht<br> <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
On Sep 5, 2009, at 7:42 AM, Ragnarok sdf wrote:<br>
<br>
> Hi<br>
> I am trying to calculate the PMF by pulling two membrane protein<br>
> monomers apart using the pull code with umbrella sampling. While<br>
> trying to generate my reaction path, no matter how slow I pull, my<br>
> helix starts bending (not really bending, but it kind of tends to<br>
> transform into a "C" shape inside my bilayer). Since I am only<br>
> simulating a small part of what would a be a very big transmembrane<br>
> receptor, I thought about restraining the movement along the z axis<br>
> of my terminal residues, sort of simulating the "weight" that would<br>
> exist if the entire intracellular and extracellular domains were<br>
> there. My protocol to obtain the PMF is to use this first pulling<br>
> protocol only to generate the different windows (distance between<br>
> the two monomers) in each of which I would use the umbrella sampling<br>
> (maintaining the force constant and switching off the pull_rate) to<br>
> generate data to perform WHAM analysis.<br>
> So that leaves me with two questions.<br>
> First is: would I, by restraining the movement along the Z axis,<br>
> create artifacts that would be computed and ruin my PMF calculation?<br>
Technically speaking, no. But you should correct for the energy of<br>
imposing the<br>
alignment with the z axis.<br>
> And second: Would this be a correct PMF protocol?<br>
That would just give you the PMF of the two transmembrane segments<br>
given their<br>
fixed relative orientations, which might be questionable in regard to<br>
its relevance<br>
but may be not!<br>
<br>
It is however strange that you have this C shape even with the slow<br>
pulling.<br>
You might want to check your parameters/procedure. You might need a long<br>
period of "relaxation/equilibration" to remove the C shape, which<br>
suggests<br>
that you are still pulling too fast!<br>
<br>
XAvier.<br>
> Thank you in advance<br>
> Fabrício Bracht<br>
</blockquote></div><br>