From: Leonardo Darre (lrdarre_at_gmail.com)
Date: Wed Dec 10 2014 - 08:08:27 CST
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
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