[gmx-users] SMD pulling question

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat May 15 15:17:54 CEST 2010

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.


> 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  
information about the goals of the SMD, it was more of a broad "just in case"

I certainly agree that the use of absolute restraints shouldn't be necessary.


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