Dear Justin:
I still disagree. I know it's a fine point, but I think it's important.
The PMF would, I presume, be created by applying a relative position
restraint along Z between the center of mass of a large ligand and the
center of mass of a bilayer and slowly changing the relative position
to which the distance is restrained.
I don't see how an absolute restraint on the COM of the bilayer would
affect the stability -- or even the dG results -- in any way. Perhaps
you're talking about using weak position restraints in X,Y,Z on, say,
the lipid phosphates? The shape of the PMF would be all wrong, but I
suppose that there are cases where this might be a good idea.
Chris.
I guess that I am missing something, but how would restraining the
position of the bilayer COM in absolute space have any affect on
anything at all? I certainly agree that one wants to observe if the
membrane has been destabilized, but if so then I think the solution
would be slower pulling and not an additional restraint on the COM of
the bilayer in absolute coordinates. Perhaps this is what you meant
Justin and I just got caught up in your word "unless".
Indeed, by "unless" I am simply considering the case that some large
molecule is
being forced against the membrane, causing it to somehow destabilize. I guess
that's a bit of a far-fetched hypothetical, but in the absence of any
additional
information about the goals of the SMD, it was more of a broad "just in case"
scenario.
I certainly agree that the use of absolute restraints shouldn't be necessary.
-Justin
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