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".
Chris.
Esteban Gabriel Vega Hissi wrote:
[Hide Quoted Text]
Hi everyone,
I have a question regarding pulling a molecule in a SMD simulation. I
pretend to translate a ligand across a lipid bilayer and get later the
PMF to calculate the DeltaG profile across the bilayer.
The reference group for pulling will be the COM of the bilayer but do I
have to restain the position of it?
In theory, no, unless by pulling you somehow manage to destabilize the
membrane
or its position. Try it and see, then determine a solution if one is
necessary.
Generally a sufficiently slow pulling rate (such that the membrane is not
destabilized) should not cause problems.
-Justin
Thanks in advance
Esteban
UNSL
Argnetina
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