[gmx-users] SMD pulling question

[chris.neale at utoronto.ca]

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:

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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