[gmx-users] SMD pulling question

Justin A. Lemkul jalemkul at vt.edu
Sat May 15 04:27:08 CEST 2010

chris.neale at utoronto.ca wrote:
> 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" 

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


> 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
> Argnetina


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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