Re: FEP with flattened free energy surface?

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
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
time-independent.
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.

Cheers,
Jerome

On 6 April 2011 11:49, Ivan Vyalov <VyalovIvan_at_yandex.ru> 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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