Ragnarok sdf
Fri, 04 Sep 2009 22:44:01 -0700
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? And second: Would this be a correct PMF protocol? Thank you in advance FabrÃcio Bracht
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