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

XAvier Periole x.periole at rug.nl
Sun Sep 6 23:03:01 CEST 2009

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

> 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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