Esteban Gabriel Vega Hissi wrote:
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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========================================
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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