Re: question about FEP for amphiphile in lipid bilayer

From: Giacomo Fiorin (
Date: Wed Dec 10 2014 - 08:41:25 CST

Have you tried also an orientation restraint?
On Dec 10, 2014 9:09 AM, "Leonardo Darre" <> wrote:

> Hi
> I intend to calculate the free energy of annihilating an amphipathic
> molecule from a POPC lipid bilayer using FEP. Because the orientation of
> the molecule should be kept unchanged during the simulation I thought of
> using two dummy atoms, one to define a distance colvar to the head of the
> amphiphile and the other to define a second distance colvar to the tail of
> the amphiphile. In this way I could compute afterwards the contribution of
> the orientational restraints to the free energy.
> May I ask for comments or recommendations about this approach?
> Thanks a lot
> Leonardo

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