[gmx-users] SMD pulling question

Justin A. Lemkul jalemkul at vt.edu
Fri May 14 23:38:49 CEST 2010

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.


> 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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