Re: FEP and solvent

From: Surjit Dixit (
Date: Thu Jun 16 2005 - 09:06:17 CDT

Hello Matthew,

While doing a FEP you would be performing the simulation long enough
for the water molecules to be displaced as you grow the ligand in a
conformation bound to the protein. So you dont need to explicitly
perturb the water moelcules. In such cases you should also be doing
constant pressure simulation to accomodate the increase in volume of
the system as you introduce the ligand and dispalce the water

Note that if you are trying to grow the complete trioligonucletoide (~
120 atoms?), this is a large system to manipulate during a FEP
simulation and you need to be careful. It might be tricky to control
this perturbation and ideally you would also need to make you
simulation windows long enough for the system to equilibrate properly
before moving to the next perturbation window. Double decomposition
simulations to calculate the binding free energy are usually are
performed on ligands which are about 50 atoms or less.

Best wishes,

On 6/12/05, Matthew Wilce <> wrote:
> Dear NAMDers
> I have been working through using FEP. I am applying it to a 100aa
> protein complexed with a trioligonucleotide. I am wondering whether I
> should be considering the solvent that is displaced by the
> oligonucleotide. In other words should I be considering someway of
> shrinking a set of water molecules that are in the position occupied
> by the oligo? Has anyone done this?
> Associate Professor Matthew Wilce
> Monash University

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