Re: FEP with flattened free energy surface?

From: Jérôme Hénin (
Date: Wed Apr 06 2011 - 11:45:29 CDT

Hi Ivan,

That should be possible. Here is how I see it:
1) run ABF to get biasing potential
2) run FEP with ABF bias, disabling updatePotential to keep the bias
In this step, save FEP data and colvars trajectory with the same
frequency (e.g. 10 timesteps) to make the next step easier
3) compute a FEP estimator with unbiased data: you need to reweight
the ensemble averages based on the applied ABF bias.


On 6 April 2011 11:49, Ivan Vyalov <> wrote:
> Hi all,
> I wonder, is it possible to perform FEP calculations with solute molecule with flattened free energy surface along several reaction coordinates?
> For instance, if I take dipeptide with conformational degrees of freedom ( dihedrals \phi & \psi ) and two minima defined by them, I should take into account this minima and do something similiar to what is described in JPhysChem 97, 3409.
> From the other hand I could run ABF, apply forces and perform FEP with flat free energy surface along these coordinates, is it possible in NAMD? Or I should do such task in a different way?
> --
> with best regards,
> Ivan

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