**From:** Jérôme Hénin (*jerome.henin_at_ibpc.fr*)

**Date:** Mon Nov 18 2013 - 17:32:09 CST

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