Re: FEP calculations: optimizing the dlambda, number of steps

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Nov 19 2013 - 04:25:39 CST

> The column before temperature is the average change in potential energy
> (deltaUavg) and the column preceding it is the change in potential energy
> (delta U). Is this correct?

Yes, that is correct.

Jerome

> On Mon, Nov 18, 2013 at 6:32 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>
> > Hi,
> >
> > AlchDecouple only makes a difference if there are nonbonded interactions
> > within the perturbed groups.
> >
> > "AlchDecouple on" means that these interactions are unperturbed, so that
> > the "intact" molecule is decoupled from its environment.
> > "AlchDecouple off" means that the molecule's nonbonded interactions
> > (included its self-interactions) are perturbed.
> >
> > Jerome
> >
> >
> > ----- Original Message -----
> > > also, can some one explain the parameter "AlchDecouple"
> > > I have done runs with both " alchDecouple on" and "alchDecouple off", but
> > > didn't notice any difference while plotting delta G vs. deltalambda
> > values.
> > >
> > > Any help will be really appreciated,
> > >
> > > thanks,
> > > Shyno
> > >
> > >
> > > On Mon, Nov 18, 2013 at 12:44 PM, Shyno Mathew <sm3334_at_columbia.edu>
> > wrote:
> > >
> > > > Hello all,
> > > > I think I figured out the answers
> > > > The column before temperature is the average change in potential energy
> > > > (deltaUavg) and the column preceding it is the change in potential
> > energy
> > > > (delta U). So I should calculate the variance of delta U values to
> > optimize
> > > > delta lambda, length of each window?
> > > > Could some one confirm this?
> > > >
> > > > thanks,
> > > > Shyno
> > > >
> > > >
> > > > On Fri, Nov 15, 2013 at 4:02 PM, Shyno Mathew <sm3334_at_columbia.edu>
> > wrote:
> > > >
> > > >> Dear all,
> > > >> I am doing the FEP calculations and need some help in understanding
> > the
> > > >> .fepout file.
> > > >> 1. this is the first part of .fepout file
> > > >> # STEP Elec vdW dE dE_avg Temp dG
> > > >>
> > > >> # l l+dl l l+dl E(l+dl)-E(l)
> > > >>
> > > >>
> > > >> #NEW FEP WINDOW: LAMBDA SET TO 0 LAMBDA2 0.05
> > > >> FepEnergy: 0 -469793 -469790 34401.03 34399.75 0.8153 0.8153 298.6998
> > > >> 0.8153 FepEnergy: 100 -472878 -472876 33902.44 33900.11 0.4059 0.3622
> > > >> 313.4741 0.1558 FepEnergy: 200 -472922 -472919 33338.32 33336.3
> > 0.8862
> > > >> 0.1122 312.7195 -0.3716
> > > >> I understand the penultimate column is temperature and the last
> > column is
> > > >> dG value. What exactly are the other columns?
> > > >>
> > > >> 2. I am trying to see what dlambda, number of steps will give me
> > accurate
> > > >> results.
> > > >> Following article says keeping the variance at each stage on the
> > order of
> > > >> 1-2 KT usually guarantees good overlap between probability
> > distributions
> > > >> in
> > > >> two consecutive strata and a reliable error estimate.
> > > >> Here the variance means the variance of dG values (only of the
> > ensemble
> > > >> average, not including minimization??) for a given lambda window?
> > > >> http://pubs.acs.org/doi/abs/10.1021/jp102971x
> > > >> (talking about page 10242 of article)
> > > >> For 300 K, 1-2 KT is 0.596 - 1.192 Kcal/mol.
> > > >> The variance (considering ensemble (not minimization values) dG
> > values
> > > >> for first window, lambd= 0 to lambda=0.05) is 0.0158. So it's one
> > order
> > > >> lower. This means I need to change dlambda and/or change the number of
> > > >> steps after minimization?
> > > >>
> > > >> thanks,
> > > >> Shyno
> > > >>
> > > >> --
> > > >> Shyno Mathew
> > > >> PhD student
> > > >> Department of Chemical Engineering
> > > >> Columbia University
> > > >>
> > > >>
> > > >
> > > >
> > > > --
> > > > Shyno Mathew
> > > > PhD student
> > > > Department of Chemical Engineering
> > > > Columbia University
> > > >
> > >
> > >
> > >
> > > --
> > > Shyno Mathew
> > > PhD student
> > > Department of Chemical Engineering
> > > Columbia University
> > >
> >
>
>
>
> --
> Shyno Mathew
> PhD student
> Department of Chemical Engineering
> Columbia University
>

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