Re: question about FEP for amphiphile in lipid bilayer

From: Leonardo Darre (
Date: Wed Dec 10 2014 - 09:20:51 CST

No I haven't. Would you recommend that option instead of using the dummy

Thanks a lot

On Wed, Dec 10, 2014 at 2:41 PM, Giacomo Fiorin <>

> 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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