[gmx-users] PMF and pull with membrane helix

Ragnarok sdf fabracht1 at gmail.com
Sat Sep 5 07:42:49 CEST 2009

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
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
Fabrício Bracht
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