[email protected] 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"
scenario.
I certainly agree that the use of absolute restraints shouldn't be necessary.
-Justin
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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