Re: question about FEP for amphiphile in lipid bilayer

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
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" <lrdarre_at_gmail.com> 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
>

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:27 CST