[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.
> 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
> or its position. Try it and see, then determine a solution if one is
> Generally a sufficiently slow pulling rate (such that the membrane is not
> destabilized) should not cause problems.
> Thanks in advance
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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