From: Ivan Vyalov (VyalovIvan_at_yandex.ru)
Date: Fri Apr 08 2011 - 14:12:38 CDT
Hi Jerome,
Thanks for reply! So, colvars config should contain lines like these:
abf {
colvars phi psi
updateBias no
inputPrefix colvarA01o
fullSamples 200
}
And then I start FEP calculations that seems to be working ( I didn't try with solvent yet ).
May I ask you one more question?
If I want to perform annihilation of dipeptide then won't I have to recalculate bias ( along \phi & \psi ) between FEP steps ( perhaps, not between every lambda window )? In my case solvent changes free energy surface quite significantly and if I have barriers ~6 kcal/mol for vacuum then for solvent they are ~16 kcal/mol.
06.04.11, 20:45, "Jérôme Hénin" <jhenin_at_ifr88.cnrs-mrs.fr>:
> 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
> >
> >
>
>
>
-- with best regards, Ivan
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